All File Changes

v346_preview to v346_preview2 (2017-02-27 to 2017-03-06) v346

• src/hg/cirm/cdw/cdwPublicSubset/cdwPublicSubset.c
  • lines changed 187, context: html, text, full: html, text
    14a1bbd02ef28ebee533c805af275ef1c0ddbf6a Wed Mar 1 18:39:53 2017 -0800
    First cut at public database subsetter.
• src/hg/cirm/cdw/cdwPublicSubset/makefile
  • lines changed 4, context: html, text, full: html, text
    14a1bbd02ef28ebee533c805af275ef1c0ddbf6a Wed Mar 1 18:39:53 2017 -0800
    First cut at public database subsetter.
• src/hg/cirm/cdw/cdwReallyRemoveFiles/cdwReallyRemoveFiles.c
  • lines changed 7, context: html, text, full: html, text
    7cf802aa0be426f0873a71aa3aff1fc5431a1935 Wed Mar 1 18:55:05 2017 -0800
    Changing submitUrl to submitDir since we are all local now.
• src/hg/cirm/cdw/utils/cdwVcfStats/cdwVcfStats.c
  • lines changed 26, context: html, text, full: html, text
    cc23704bb98100f88c225f05f30b8613ba6cf354 Wed Mar 1 18:55:59 2017 -0800
    Got rid of some old slow unused code.
• src/hg/hgBlat/hgBlat.c
  • lines changed 6, context: html, text, full: html, text
    274f486bafdea10f8069c70e4159f24b49c366fe Wed Mar 1 16:37:04 2017 -0800
    Fixing some bizarre styling on hgBlat when it asks if you want to make a custom track of results. Only html printf changes, refs #2811
• src/hg/hgChooseDb/hgChooseDb.c
  • lines changed 2, context: html, text, full: html, text
    782c81418b4a7b3194393adf3efde7b868b61589 Wed Mar 1 11:54:05 2017 -0800
    Replacing some more hardcoded ../js/ paths with calls to jsIncludeFile.
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
  • lines changed 3, context: html, text, full: html, text
    782c81418b4a7b3194393adf3efde7b868b61589 Wed Mar 1 11:54:05 2017 -0800
    Replacing some more hardcoded ../js/ paths with calls to jsIncludeFile.
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 2, context: html, text, full: html, text
    782c81418b4a7b3194393adf3efde7b868b61589 Wed Mar 1 11:54:05 2017 -0800
    Replacing some more hardcoded ../js/ paths with calls to jsIncludeFile.
• src/hg/hgPublicSessions/hgPublicSessions.c
  • lines changed 7, context: html, text, full: html, text
    5538755f556a081861b4b715ca6cc70fbc49ec7c Fri Feb 24 16:36:25 2017 -0800
    hgSession and PublicSessions should now work when gbMembers is remote, refs #18800
• src/hg/hgSession/hgSession.c
  • lines changed 30, context: html, text, full: html, text
    5538755f556a081861b4b715ca6cc70fbc49ec7c Fri Feb 24 16:36:25 2017 -0800
    hgSession and PublicSessions should now work when gbMembers is remote, refs #18800
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    658fc795c84d9110bdfa444fc9eede842322759a Wed Mar 1 17:14:13 2017 -0800
    Don't allow ',' in download file name -- replace with '.'. refs #18931
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    29e50f56b4a784d2c37d48a9361d02e70638375e Wed Mar 1 12:14:41 2017 -0800
    add an assert to make sure we catch a potential trashed data situation #18950
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    eddcc31f5787c57ae35557080913eb2ca74dfdb1 Thu Mar 2 11:29:03 2017 -0800
    adding keyboard shortcuts ma/mc/mn and also one more button to the highlight dialog, refs #18936
  • lines changed 3, context: html, text, full: html, text
    0ec7a2cf0fe8d4078b875c54c8583faeb4bcf802 Thu Mar 2 16:52:03 2017 -0800
    changing keyboard shortcuts for highlights, refs #18986
  • lines changed 3, context: html, text, full: html, text
    05045ac1625397ef12d688d245cf27e920f64d72 Fri Mar 3 10:28:16 2017 -0800
    fixing a small bug that appears with an empt cart in the new highlight shortcut, refs #18936
• src/hg/hgTracks/searchTracks.c
  • lines changed 32, context: html, text, full: html, text
    690fa17cbf29efbe0f1b6c9b724f4e3614a615fb Thu Mar 2 23:23:09 2017 -0800
    fixes #18981. track search js problems from CSP2 changes. Needed to add id to some functions in cheapcgi.c and hui.c.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    f50a54ddd5728460bd8dd33a5fccd6fa3e84eef6 Wed Mar 1 12:25:33 2017 -0800
    correct colors on scaffold names when in chain tracks refs #18656
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 3, context: html, text, full: html, text
    ae0555edbf3e9bf3d9e05d57786f801ddabe82ee Wed Mar 1 12:31:11 2017 -0800
    put out a warning if maf summary information is missing, but needed #18950
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    ccde18340106a9271a08a355169229beaeb43f92 Tue Feb 28 15:00:36 2017 -0800
    Correcting a typo around a displayed paragraph html tag on FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    4ed752271aacbe0426428c64e27933a7f8be9153 Thu Mar 2 08:41:13 2017 -0800
    Added melGal5 to releases.html per refs #18739
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 5, context: html, text, full: html, text
    7e0c8f7c90f05e0464dcdf861ac91abc9281a544 Thu Mar 2 08:11:38 2017 -0800
    Edited the credtis per refs #18739
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 30, context: html, text, full: html, text
    735c7bae11c90c74a2e7fad1af1250968c7d8fe3 Fri Mar 3 11:17:13 2017 -0800
    Adding announcement for NCBI RefSeq track, refs #13673
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 2, context: html, text, full: html, text
    248bb52ea0732f4970ccc83c91f8cfe54d633e22 Tue Feb 28 13:04:52 2017 -0800
    Adding PMCID to 2017 NAR, refs #18944
• src/hg/htdocs/images/Rhinopithecus_bieti.jpg
  • lines changed 0, context: html, text, full: html, text
    7e7c8cb7221ae305e6fa2454f5377b15ffb2c4f6 Tue Feb 28 10:33:54 2017 -0800
    (C) Copyright Jacky Poon, all rights reserved - http://www.jackypoon.org/mystery-monkeys
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 7, context: html, text, full: html, text
    ffce37768c3211b8b87a9a53ed7aba8551c77cf7 Wed Mar 1 12:12:07 2017 -0800
    Re-removing vestigial script (pre-CSP2) that was required for v344 and earlier CGIs, now that v345 has been released on the RR. (The script was originally removed in Galt's big CSP commit a53b9958, then added back in fb27495f to support v344 CGIs on the RR.) refs #18686 notes 25-28, 37-48
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    735c7bae11c90c74a2e7fad1af1250968c7d8fe3 Fri Mar 3 11:17:13 2017 -0800
    Adding announcement for NCBI RefSeq track, refs #13673
• src/hg/inc/hui.h
  • lines changed 6, context: html, text, full: html, text
    690fa17cbf29efbe0f1b6c9b724f4e3614a615fb Thu Mar 2 23:23:09 2017 -0800
    fixes #18981. track search js problems from CSP2 changes. Needed to add id to some functions in cheapcgi.c and hui.c.
• src/hg/inc/sessionThumbnail.h
  • lines changed 5, context: html, text, full: html, text
    5538755f556a081861b4b715ca6cc70fbc49ec7c Fri Feb 24 16:36:25 2017 -0800
    hgSession and PublicSessions should now work when gbMembers is remote, refs #18800
• src/hg/js/hgTracks.js
  • lines changed 38, context: html, text, full: html, text
    eddcc31f5787c57ae35557080913eb2ca74dfdb1 Thu Mar 2 11:29:03 2017 -0800
    adding keyboard shortcuts ma/mc/mn and also one more button to the highlight dialog, refs #18936
  • lines changed 2, context: html, text, full: html, text
    c315c738489bdd9029742f0a58dae14cc4b98e09 Thu Mar 2 11:41:07 2017 -0800
    adding some doc about new keyboard shortcut, refs #18936
  • lines changed 6, context: html, text, full: html, text
    05045ac1625397ef12d688d245cf27e920f64d72 Fri Mar 3 10:28:16 2017 -0800
    fixing a small bug that appears with an empt cart in the new highlight shortcut, refs #18936
• src/hg/js/jquery.plugins.js
  • lines changed 305, context: html, text, full: html, text
    5372bb9c25e614b2cfa429f35d8e4470176fd6be Wed Mar 1 12:27:01 2017 -0800
    Removing vestigial Drupal javascript. The entire remaining function of the Drupal object was to store two parameters for SuperFish (delay and speed). Now we just set the two parameters to the previously Drupal-stored values. refs #18686 notes 42, 48.
• src/hg/lib/hCommon.c
  • lines changed 14, context: html, text, full: html, text
    4941d34ac775c6f2e82434867b9e7823387238c1 Sun Mar 5 15:04:00 2017 -0800
    fixes #18983. hUserAbort in hg/lib/hCommon.c was not working right. In particular, although it sort of worked for errAbort, it did not work for hUserAbort. Hopefully this is now working better than ever.
• src/hg/lib/hui.c
  • lines changed 7, context: html, text, full: html, text
    690fa17cbf29efbe0f1b6c9b724f4e3614a615fb Thu Mar 2 23:23:09 2017 -0800
    fixes #18981. track search js problems from CSP2 changes. Needed to add id to some functions in cheapcgi.c and hui.c.
• src/hg/lib/jsHelper.c
  • lines changed 16, context: html, text, full: html, text
    782c81418b4a7b3194393adf3efde7b868b61589 Wed Mar 1 11:54:05 2017 -0800
    Replacing some more hardcoded ../js/ paths with calls to jsIncludeFile.
• src/hg/lib/sessionThumbnail.c
  • lines changed 22, context: html, text, full: html, text
    5538755f556a081861b4b715ca6cc70fbc49ec7c Fri Feb 24 16:36:25 2017 -0800
    hgSession and PublicSessions should now work when gbMembers is remote, refs #18800
• src/hg/lib/trashDir.c
  • lines changed 1, context: html, text, full: html, text
    5538755f556a081861b4b715ca6cc70fbc49ec7c Fri Feb 24 16:36:25 2017 -0800
    hgSession and PublicSessions should now work when gbMembers is remote, refs #18800
• src/hg/lib/web.c
  • lines changed 25, context: html, text, full: html, text
    07ec0c309cf5c4da98b99f8d2a596ea261151714 Mon Feb 27 11:04:54 2017 -0800
    Cleaning up after myself, refs #18948
• src/hg/makeDb/doc/colAng1/initialBuild.txt
  • lines changed 116, context: html, text, full: html, text
    a2f718591b34d7d49f661232ace1172be6e004a7 Thu Mar 2 15:35:12 2017 -0800
    colAng1 in the pushQ refs #17545
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 147, context: html, text, full: html, text
    3320e55d59f033e6af9d920c365bb51bda880c66 Fri Mar 3 14:52:08 2017 -0800
    chainNet for colAng1 and macNem1 refs #17545
• src/hg/makeDb/doc/micMur3/initialBuild.txt
  • lines changed 748, context: html, text, full: html, text
    253b4ed65baa32bbe58c399a4fda94916c9ac928 Thu Mar 2 14:39:43 2017 -0800
    starting micMur3 browser build refs #18984
• src/hg/makeDb/doc/mm10.txt
  • lines changed 128, context: html, text, full: html, text
    32ac8a3e93bdbc7e8c9cfaabb45be61a84b9c197 Wed Mar 1 14:30:47 2017 -0800
    adding lastz chain net for macNem1 and colAng1 refs #17545 #18927
• src/hg/makeDb/doc/nasLar1/initialBuild.txt
  • lines changed 13, context: html, text, full: html, text
    64b49d1b1d01376e06772754ac94d4b802cd1c3e Mon Feb 27 10:27:02 2017 -0800
    add augustusGene build procedure refs #14437
• src/hg/makeDb/doc/panPan2/initialBuild.txt
  • lines changed 17, context: html, text, full: html, text
    92f13b481d2017d01d64daaa69c6caefef939867 Mon Feb 27 13:09:35 2017 -0800
    indicate what happend with lastz gorGor and add chromAlias table refs #16036
• src/hg/makeDb/doc/panPan2/lastzRuns.txt
  • lines changed 2, context: html, text, full: html, text
    92f13b481d2017d01d64daaa69c6caefef939867 Mon Feb 27 13:09:35 2017 -0800
    indicate what happend with lastz gorGor and add chromAlias table refs #16036
• src/hg/makeDb/doc/rhiBie1/initialBuild.txt
  • lines changed 744, context: html, text, full: html, text
    4d1ef500be04d162afa23585bdd663a504fc7ae1 Tue Feb 28 14:33:15 2017 -0800
    beginning build for rhiBie1 refs #18958
  • lines changed 177, context: html, text, full: html, text
    10c4006f6c96cefd3c4fd870e91a218611e9d7e8 Thu Mar 2 10:03:29 2017 -0800
    ready for genbank run refs #18958
• src/hg/makeDb/genbank/etc/align-genbank
  • lines changed 3, context: html, text, full: html, text
    9ef57dd44317eeeffe88bcc4b12f0f825cbb4dae Wed Mar 1 15:55:25 2017 -0800
    move genbank build directory to /data
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 3, context: html, text, full: html, text
    4fa8a75ba2ed2551de9b4b962a45c1a8786a40a7 Mon Mar 6 09:37:57 2017 -0800
    adding rhiBie1 macNem1 micMur3 refs #18984 #18958 #18927
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    a598020325c86675e7fe212493fa1f150b0aada6 Mon Feb 27 11:14:27 2017 -0800
    Added macNem1; refs #18927
  • lines changed 19, context: html, text, full: html, text
    ed8ae5d1bd6e510a54ce663301c67fbedbca990a Wed Mar 1 15:34:51 2017 -0800
    Added rhiBie1; refs #18958
  • lines changed 20, context: html, text, full: html, text
    d941d7db26da086ab15f4c2c3767744ca92b8737 Sat Mar 4 16:44:38 2017 -0800
    adding micMur3 Mouse lemur refs #18984
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 4, context: html, text, full: html, text
    4fa8a75ba2ed2551de9b4b962a45c1a8786a40a7 Mon Mar 6 09:37:57 2017 -0800
    adding rhiBie1 macNem1 micMur3 refs #18984 #18958 #18927
• src/hg/makeDb/genbank/etc/mkdownload
  • lines changed 1, context: html, text, full: html, text
    9ef57dd44317eeeffe88bcc4b12f0f825cbb4dae Wed Mar 1 15:55:25 2017 -0800
    move genbank build directory to /data
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    74e97e338c1d8e2cd6c8ea3ac7782ffcda66f801 Mon Mar 6 09:52:37 2017 -0800
    adding rhiRox1 to genbank updates
• src/hg/makeDb/genbank/makefile
  • lines changed 2, context: html, text, full: html, text
    f518a8631e7ae69b8507db27e2514e8b1fd29048 Wed Mar 1 15:58:24 2017 -0800
    move genbank build directory to /data
• src/hg/makeDb/genbank/src/align/gbAlignSetup
  • lines changed 2, context: html, text, full: html, text
    c3c466234502ecee02738c5084ba3c7f9db6080c Thu Mar 2 06:28:57 2017 -0800
    move genbank build directory to /data
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    a598020325c86675e7fe212493fa1f150b0aada6 Mon Feb 27 11:14:27 2017 -0800
    Added macNem1; refs #18927
  • lines changed 2, context: html, text, full: html, text
    ed8ae5d1bd6e510a54ce663301c67fbedbca990a Wed Mar 1 15:34:51 2017 -0800
    Added rhiBie1; refs #18958
• src/hg/makeDb/schema/all.joiner
  • lines changed 10, context: html, text, full: html, text
    2155f55ea01c48f279fffc5d2aba9027eff7e39d Mon Feb 27 13:37:45 2017 -0800
    adding macNem1 rules refs #18927
  • lines changed 10, context: html, text, full: html, text
    861d3471788fcc1fddbb6daa4e15a260a9016945 Mon Mar 6 09:43:52 2017 -0800
    adding rhiBie1 rules refs #18958
• src/hg/makeDb/trackDb/cat/felCat8/trackDb.chainNet.ra
  • lines changed 18, context: html, text, full: html, text
    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/makeDb/trackDb/cat/felCat8/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/makeDb/trackDb/chainNet.html
  • lines changed 1, context: html, text, full: html, text
    b0a11db72cfc7f65c860880a6ebf6b5bf179408f Thu Mar 2 15:13:29 2017 -0800
    Escaping some quotes, refs #18656
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    92873e9a3d1d4f1cebbed5f554c2da9d2747924f Tue Feb 28 15:17:44 2017 -0800
    removing beta release tag for old refGene track on hg38, refs #13673
  • lines changed 5, context: html, text, full: html, text
    6481b5532d0c82a44c7858c8b5ed20e5e693501f Wed Mar 1 13:04:39 2017 -0800
    Removing stanza for old style refGene track for hg38. Removing release tags from refSeqComposite for hg38 so it shows up everywhere, refs #13673
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    be1fe37bf7d0ca071f4baa0a1ce111e888c68d0e Tue Feb 28 15:12:50 2017 -0800
    Removing release tags from refSeqComposite.ra file, moving them to include statement, refs #13673
  • lines changed 1, context: html, text, full: html, text
    6481b5532d0c82a44c7858c8b5ed20e5e693501f Wed Mar 1 13:04:39 2017 -0800
    Removing stanza for old style refGene track for hg38. Removing release tags from refSeqComposite for hg38 so it shows up everywhere, refs #13673
• src/hg/makeDb/trackDb/macaca/macNem1/trackDb.chainNet.ra
  • lines changed 11, context: html, text, full: html, text
    db8181a3700622923e24fa8fe9eac8ccea739498 Fri Mar 3 15:03:42 2017 -0800
    adding chainNet overrides refs #18927
• src/hg/makeDb/trackDb/macaca/macNem1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    db8181a3700622923e24fa8fe9eac8ccea739498 Fri Mar 3 15:03:42 2017 -0800
    adding chainNet overrides refs #18927
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    68742ea2dbdb41a5130aa078aeb13993b8b66837 Tue Feb 28 14:28:41 2017 -0800
    rhiBie1 - black snub-nosed monkey - Rhinopithecus bieti refs #18958
  • lines changed 1, context: html, text, full: html, text
    dee5ba96ef4b1037785e606132aec623f521e12f Thu Mar 2 14:07:38 2017 -0800
    adding micMur3 to the build refs #18984
• src/hg/makeDb/trackDb/micOch/micOch1/trackDb.chainNet.ra
  • lines changed 29, context: html, text, full: html, text
    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/makeDb/trackDb/micOch/micOch1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    0d875ab934634962b3355d100af255d920b81319 Wed Mar 1 07:12:10 2017 -0800
    Adding release tag to refSeqComposite include statement, no redmine
• src/hg/makeDb/trackDb/mouseLemur/micMur3/description.html
  • lines changed 64, context: html, text, full: html, text
    dee5ba96ef4b1037785e606132aec623f521e12f Thu Mar 2 14:07:38 2017 -0800
    adding micMur3 to the build refs #18984
• src/hg/makeDb/trackDb/mouseLemur/micMur3/gap.html
  • lines changed 30, context: html, text, full: html, text
    dee5ba96ef4b1037785e606132aec623f521e12f Thu Mar 2 14:07:38 2017 -0800
    adding micMur3 to the build refs #18984
• src/hg/makeDb/trackDb/mouseLemur/micMur3/gold.html
  • lines changed 34, context: html, text, full: html, text
    dee5ba96ef4b1037785e606132aec623f521e12f Thu Mar 2 14:07:38 2017 -0800
    adding micMur3 to the build refs #18984
• src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    dee5ba96ef4b1037785e606132aec623f521e12f Thu Mar 2 14:07:38 2017 -0800
    adding micMur3 to the build refs #18984
• src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/trackDb.chainNet.ra
  • lines changed 11, context: html, text, full: html, text
    246124caaad43fc1cc1a402cdd7ff22603ceb8a6 Fri Mar 3 14:31:45 2017 -0800
    adding chainNet overrides for colAng1 refs #17545
• src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    246124caaad43fc1cc1a402cdd7ff22603ceb8a6 Fri Mar 3 14:31:45 2017 -0800
    adding chainNet overrides for colAng1 refs #17545
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • lines changed 195, context: html, text, full: html, text
    f3036445231924a66d82ccf888212adca93f0060 Thu Mar 2 14:24:48 2017 -0800
    new trackDb.chainNet.ra up to date with everything refs #18656
  • lines changed 7, context: html, text, full: html, text
    dee1684115f2dfea4e154de809fa9844aa8c67a7 Thu Mar 2 14:36:36 2017 -0800
    correct release tags for all chain nets in monDom5 refs #18656
• src/hg/makeDb/trackDb/panda/ailMel1/trackDb.chainNet.ra
  • lines changed 84, context: html, text, full: html, text
    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/makeDb/trackDb/platypus/ornAna2/trackDb.chainNet.ra
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    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/makeDb/trackDb/platypus/ornAna2/trackDb.ra
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    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.chainNet.ra
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    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/makeDb/trackDb/rat/rn6/ratChainNet.html
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    1eac349c7e42248061f7e87e56cc4bafa1503956 Thu Mar 2 14:42:47 2017 -0800
    Replacing the " character with the html name, refs #18656
• src/hg/makeDb/trackDb/refSeqComposite.html
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    49d799b6548c181d3ec771506618dd98780eab8f Mon Feb 27 13:50:43 2017 -0800
    Made a few edits and fixed a few typos. Refs #13673
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    0543a8c9e1f0385a15a819538e1b43d3e16328d7 Mon Feb 27 16:47:44 2017 -0800
    Moved RefSeq Other out of table list, per Hiram. Matt will add access info. Refs #13673
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    d224475ae436bae55e274b219299279d64da2c4d Tue Feb 28 12:54:35 2017 -0800
    Changing mRNA to RNA. Adding a few sentences to Data Access section about downloading bigBed data, refs #13673
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    83559955ae67c0bc4cf3a0260a245200fa140753 Tue Feb 28 14:53:51 2017 -0800
    Moving location of bigBedToBed seciton and removing some dev notes, refs #13673
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    0274b2c0c2951ebacc2b047ffa7774590466bcc6 Wed Mar 1 07:05:59 2017 -0800
    Fixing minor grammar error, refs #13673
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    107444a09d0db59fa5c29d90a3426595de926f81 Wed Mar 1 09:13:09 2017 -0800
    Minor correction, refs #13673
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    be1fe37bf7d0ca071f4baa0a1ce111e888c68d0e Tue Feb 28 15:12:50 2017 -0800
    Removing release tags from refSeqComposite.ra file, moving them to include statement, refs #13673
• src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/description.html
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    68742ea2dbdb41a5130aa078aeb13993b8b66837 Tue Feb 28 14:28:41 2017 -0800
    rhiBie1 - black snub-nosed monkey - Rhinopithecus bieti refs #18958
• src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/gap.html
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    68742ea2dbdb41a5130aa078aeb13993b8b66837 Tue Feb 28 14:28:41 2017 -0800
    rhiBie1 - black snub-nosed monkey - Rhinopithecus bieti refs #18958
• src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/gold.html
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    68742ea2dbdb41a5130aa078aeb13993b8b66837 Tue Feb 28 14:28:41 2017 -0800
    rhiBie1 - black snub-nosed monkey - Rhinopithecus bieti refs #18958
• src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/trackDb.ra
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    68742ea2dbdb41a5130aa078aeb13993b8b66837 Tue Feb 28 14:28:41 2017 -0800
    rhiBie1 - black snub-nosed monkey - Rhinopithecus bieti refs #18958
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    d5097d97a30fb5771534e424f2ea3fec6dc1f34b Thu Mar 2 10:01:52 2017 -0800
    add search rule for gold track refs #18958
• src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra
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    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
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    dee1684115f2dfea4e154de809fa9844aa8c67a7 Thu Mar 2 14:36:36 2017 -0800
    correct release tags for all chain nets in monDom5 refs #18656
• src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra
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    dee1684115f2dfea4e154de809fa9844aa8c67a7 Thu Mar 2 14:36:36 2017 -0800
    correct release tags for all chain nets in monDom5 refs #18656
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
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    484f89767f9ad8a920db835d18f90bc98ac77ea7 Wed Mar 1 14:54:58 2017 -0800
    add chainNet for macNem1 rhiBie1 colAng1 refs #18927 #18958 #17545
• src/hg/makeDb/trackDb/turkey/melGal5/description.html
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    e18170001d02c83b45feb8768513b31aa8899940 Wed Mar 1 10:11:32 2017 -0800
    edited link on description.html per refs #18739
• src/hg/makeDb/trackDb/turkey/melGal5/trackDb.chainNet.ra
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    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/makeDb/trackDb/turkey/melGal5/trackDb.ra
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    e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800
    adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
• src/hg/utils/automation/addScores.pl
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    7f3efddb472b5ebbe47532424b65ce293c92af96 Thu Mar 2 11:40:13 2017 -0800
    script to add chainNet override trackDb entries refs #18656
• src/hg/utils/automation/makePushQSql.pl
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    af0fc1c89e45db46dfd76d1637ad02b68f5dad6e Thu Mar 2 15:17:14 2017 -0800
    fixup standard list of infrastructure tables refs #17545
• src/hg/utils/buildReleaseLog/buildReleaseLog.c
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    af2d5597168427a6ff4b85dd8aeda9a0c4bd0b63 Fri Mar 3 16:25:45 2017 -0800
    Initial commit of new utility to build release log from redmine, refs #3500
• src/hg/utils/buildReleaseLog/htmlOut.c
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    af2d5597168427a6ff4b85dd8aeda9a0c4bd0b63 Fri Mar 3 16:25:45 2017 -0800
    Initial commit of new utility to build release log from redmine, refs #3500
• src/hg/utils/buildReleaseLog/htmlOut.h
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    af2d5597168427a6ff4b85dd8aeda9a0c4bd0b63 Fri Mar 3 16:25:45 2017 -0800
    Initial commit of new utility to build release log from redmine, refs #3500
• src/hg/utils/buildReleaseLog/makefile
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    af2d5597168427a6ff4b85dd8aeda9a0c4bd0b63 Fri Mar 3 16:25:45 2017 -0800
    Initial commit of new utility to build release log from redmine, refs #3500
• src/hg/utils/makefile
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    2da864ea03bfb22566351e2d0dd853118168637d Fri Mar 3 16:32:09 2017 -0800
    Adding buildReleaseLog to hg/utils makefile, refs #3500
• src/hg/utils/phyloTrees/199way.nh
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    7a0259e335a296b55b748ecc5e0a05196f29875d Fri Mar 3 10:51:16 2017 -0800
    catching up the primates refs #17545
• src/hg/utils/phyloTrees/209way.commonNames.nh
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    ddb0eb195e5d5b4d53e6e55aef9cb4d2e61d03f8 Fri Mar 3 15:41:13 2017 -0800
    catching up names for primates and mammals refs #17545
• src/hg/utils/phyloTrees/209way.dissect.txt
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    2b3b58dab5475ebf604224eec335e3580cce73e8 Fri Mar 3 14:32:27 2017 -0800
    up to date with mammals and primates refs #17545
• src/hg/utils/phyloTrees/209way.nh
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    0aa47108fc01ebc82c08dd355810308afa6a8041 Fri Mar 3 12:00:35 2017 -0800
    catching up with all mammals refs #17545
• src/hg/utils/phyloTrees/209way.scientificNames.nh
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    ddb0eb195e5d5b4d53e6e55aef9cb4d2e61d03f8 Fri Mar 3 15:41:13 2017 -0800
    catching up names for primates and mammals refs #17545
• src/hg/utils/phyloTrees/209wayChainNet.pl
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    2b3b58dab5475ebf604224eec335e3580cce73e8 Fri Mar 3 14:32:27 2017 -0800
    up to date with mammals and primates refs #17545
• src/hg/utils/phyloTrees/commonNames.sh
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    3250e238380a526eef96db6efa7d948ae467b7c6 Fri Mar 3 14:17:45 2017 -0800
    catch up mammal and primate common names refs #17545
• src/hg/utils/phyloTrees/scientificNames.sh
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    f4991091a1f033d3bb69e777b4a989a552cfa9ec Fri Mar 3 13:17:25 2017 -0800
    catching up with the primates and mammals refs #17545
• src/inc/cheapcgi.h
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    690fa17cbf29efbe0f1b6c9b724f4e3614a615fb Thu Mar 2 23:23:09 2017 -0800
    fixes #18981. track search js problems from CSP2 changes. Needed to add id to some functions in cheapcgi.c and hui.c.
• src/lib/cheapcgi.c
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    690fa17cbf29efbe0f1b6c9b724f4e3614a615fb Thu Mar 2 23:23:09 2017 -0800
    fixes #18981. track search js problems from CSP2 changes. Needed to add id to some functions in cheapcgi.c and hui.c.
• src/lib/tagStorm.c
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    0112fcaa33e4a0c803371bab77a1d3a369c7f72b Mon Feb 6 12:49:54 2017 -0800
    Making tagStanzaUpdateTag put new tags at the end, and also make a verbose message when updating existing tags rather than adding new ones.
• src/lib/vcf.c
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    929046d9e4afc5c5f8821cd7acd7cc4e3c48dc00 Wed Mar 1 18:57:11 2017 -0800
    Upping a buffer size so that some Snyder lab VCF files would parse.
• src/tagStorm/tagStormCheck/tagStormCheck.c
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    d3e3fba3ca8d8badc78ffdf39897169900b0a91a Wed Mar 1 10:07:48 2017 -0800
    Fixing a bug where things not in schema were tested against last wildcard containing tag specification in schema.
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
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    4de4a6a4b26b6555e09b05633795051e93099052 Mon Jan 30 10:57:41 2017 -0800
    Further improving comment that explains overall algorithm.
• src/tagStorm/tagStormInfo/tagStormInfo.c
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    f84ef13fe3ea2889a2a84cc136a0a93f3181ed40 Wed Mar 1 18:57:35 2017 -0800
    Improved usage message
• src/tagStorm/tagStormJoinTab/tagStormJoinTab.c
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    04d3a51e6b6e93ca59b5f01d29da7dd5cd907ab0 Mon Feb 6 12:50:49 2017 -0800
    Making it so that the append option will update the value of existing tags rather than making new tags.
• src/tagStorm/tagStormReformat/tagStormReformat.c
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    aa084934a19cfef4313f17a2a952c8d3e81070c9 Wed Mar 1 18:58:00 2017 -0800
    Added sort and sortOn options.
• src/utils/qa/weeklybld/buildEnv.csh
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    428279f27f702e6fcc17394a3b1dfa21d6920dca Mon Mar 6 10:23:05 2017 -0800
    v346 preview2 refs #18964
• src/utils/tabQuery/tabQuery.c
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    6d140e6f65c1491b7f6ae406bc4f0acf82cc41d1 Wed Feb 15 12:07:25 2017 -0800
    Making it accept wildcards in field list.

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