All File Changes

v378_preview2 to v378_base (2019-02-18 to 2019-02-25) v378

• src/hg/hgSession/backup.c
  • lines changed 100, context: html, text, full: html, text
    7ac21bf1c3ef2b54beec22d23f6a6d389e229d92 Thu Feb 21 02:25:27 2019 -0800
    fixing it to handle 0 custom tracks to backup by skipping the backup button. Fixed the show to match the make and correctly deal with both complete custom-trash-table types as well as newer bigDataUrl cts. Also fixed a bug where the origTrackLine is missing from CTs generated by Table Browser. Currently just try to detect the missing value, and if tdbType is wig then feed in a simple track line for generic wiggles.
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 2, context: html, text, full: html, text
    5fa4c7cf103bf3323dfbc5a06f666b264870503f Fri Feb 22 14:05:53 2019 -0800
    don't look in database for bigWig table if assembly hub #22979
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 9, context: html, text, full: html, text
    abd8fbef66db16fc94e809184413ca69bba0d1e9 Tue Feb 19 09:50:20 2019 -0800
    Working on unreleased FAQ genes page ref#22696
  • lines changed 9, context: html, text, full: html, text
    5e4c5867d5a5b041bbaaa72dea9236c7bbb0fbf8 Tue Feb 19 14:20:38 2019 -0800
    Accidentally inserted the ENCODE section after the anniversary title section, refs #20314
  • lines changed 28, context: html, text, full: html, text
    b5769f19a15e1303d34cab3fa6723695bd8339cb Fri Feb 22 02:30:41 2019 -0800
    another genes FAQ update, refs #22696
  • lines changed 35, context: html, text, full: html, text
    7436ba6b6f1a5face1e99b98506d84157413403b Mon Feb 25 06:03:28 2019 -0800
    Adding SHANK2/3 example to faqgenes, refs #22970
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 75, context: html, text, full: html, text
    137b12a8d895e882053a8bca18d09a9158788af6 Fri Feb 22 17:47:35 2019 -0800
    Updating documentation on the CT Backup feature
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 24, context: html, text, full: html, text
    8a2717b10711d854c7dcee5ffc41dc2a60624c72 Tue Feb 19 16:23:15 2019 -0800
    Adding RefSeq HGMD annoucement to newsarch.html and indexNew.html, refs #22659
  • lines changed 1, context: html, text, full: html, text
    46a6f6ef1c2bb13b12446ac133ed07853fec1474 Tue Feb 19 16:28:01 2019 -0800
    edits to newsarch.html, refs #22659
  • lines changed 0, context: html, text, full: html, text
    f1180903c169be8ed1370e1c07ddbb5107a3ef60 Wed Feb 20 09:52:03 2019 -0800
    editing newarch.html for refSeq HGMD, refs #22659
• src/hg/htdocs/history.html
  • lines changed 114, context: html, text, full: html, text
    a1215908f433eb877091ffc6ab770b3a9333fab8 Tue Feb 19 09:11:20 2019 -0800
    Moving the ENCODE section before the 10 year anniversary section, refs #20314
  • lines changed 18, context: html, text, full: html, text
    5e4c5867d5a5b041bbaaa72dea9236c7bbb0fbf8 Tue Feb 19 14:20:38 2019 -0800
    Accidentally inserted the ENCODE section after the anniversary title section, refs #20314
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    8a2717b10711d854c7dcee5ffc41dc2a60624c72 Tue Feb 19 16:23:15 2019 -0800
    Adding RefSeq HGMD annoucement to newsarch.html and indexNew.html, refs #22659
• src/hg/htdocs/training/index.html
  • lines changed 15, context: html, text, full: html, text
    2840f5306ad9d60ce4fc48e94ce36d050fbfa061 Fri Feb 15 16:40:10 2019 -0800
    removing completed HudsonAlpha workshop and moving Costa Rica into active list
  • lines changed 13, context: html, text, full: html, text
    f952341e17bdb3fda1b5236dfb799cd8aed60220 Tue Feb 19 09:24:27 2019 -0800
    adding links for singapore workshop
  • lines changed 28, context: html, text, full: html, text
    5e4c5867d5a5b041bbaaa72dea9236c7bbb0fbf8 Tue Feb 19 14:20:38 2019 -0800
    Accidentally inserted the ENCODE section after the anniversary title section, refs #20314
  • lines changed 3, context: html, text, full: html, text
    3b2efe894dde828e57bb0c5097f5e4b18ef871f7 Mon Feb 25 07:32:30 2019 -0800
    adding link to signup for Costa Rica workshop. Fixing broken link to Wisconsin workshop
• src/hg/hubApi/apiUtils.c
  • lines changed 18, context: html, text, full: html, text
    4061e76e6ead3d4a59704aab422abef16e3cfd2e Tue Feb 19 11:41:29 2019 -0800
    beginning to return data from track hub bigBed files refs #18869
  • lines changed 18, context: html, text, full: html, text
    5e4c5867d5a5b041bbaaa72dea9236c7bbb0fbf8 Tue Feb 19 14:20:38 2019 -0800
    Accidentally inserted the ENCODE section after the anniversary title section, refs #20314
• src/hg/hubApi/dataApi.h
  • lines changed 3, context: html, text, full: html, text
    4061e76e6ead3d4a59704aab422abef16e3cfd2e Tue Feb 19 11:41:29 2019 -0800
    beginning to return data from track hub bigBed files refs #18869
  • lines changed 3, context: html, text, full: html, text
    5e4c5867d5a5b041bbaaa72dea9236c7bbb0fbf8 Tue Feb 19 14:20:38 2019 -0800
    Accidentally inserted the ENCODE section after the anniversary title section, refs #20314
• src/hg/hubApi/getData.c
  • lines changed 154, context: html, text, full: html, text
    4061e76e6ead3d4a59704aab422abef16e3cfd2e Tue Feb 19 11:41:29 2019 -0800
    beginning to return data from track hub bigBed files refs #18869
  • lines changed 154, context: html, text, full: html, text
    5e4c5867d5a5b041bbaaa72dea9236c7bbb0fbf8 Tue Feb 19 14:20:38 2019 -0800
    Accidentally inserted the ENCODE section after the anniversary title section, refs #20314
  • lines changed 70, context: html, text, full: html, text
    eda78578a5c610db7acf00034b8823d6e9b96383 Tue Feb 19 14:39:21 2019 -0800
    returning any and all data from bigBed track refs #18869
  • lines changed 53, context: html, text, full: html, text
    e811848a75708cf437ed474e23a5997a29007aa7 Tue Feb 19 18:34:33 2019 -0800
    bigBed and bigWig hub data output examples refs #18869
• src/hg/hubApi/hubApi.c
  • lines changed 3, context: html, text, full: html, text
    4061e76e6ead3d4a59704aab422abef16e3cfd2e Tue Feb 19 11:41:29 2019 -0800
    beginning to return data from track hub bigBed files refs #18869
  • lines changed 3, context: html, text, full: html, text
    5e4c5867d5a5b041bbaaa72dea9236c7bbb0fbf8 Tue Feb 19 14:20:38 2019 -0800
    Accidentally inserted the ENCODE section after the anniversary title section, refs #20314
  • lines changed 6, context: html, text, full: html, text
    eda78578a5c610db7acf00034b8823d6e9b96383 Tue Feb 19 14:39:21 2019 -0800
    returning any and all data from bigBed track refs #18869
  • lines changed 3, context: html, text, full: html, text
    e811848a75708cf437ed474e23a5997a29007aa7 Tue Feb 19 18:34:33 2019 -0800
    bigBed and bigWig hub data output examples refs #18869
  • lines changed 146, context: html, text, full: html, text
    7f4579f5b69be16ca391924dce94d17599db2873 Mon Feb 25 09:49:27 2019 -0800
    counting up track types for UCSC db same as hub refs #18869
• src/hg/hubApi/list.c
  • lines changed 13, context: html, text, full: html, text
    4061e76e6ead3d4a59704aab422abef16e3cfd2e Tue Feb 19 11:41:29 2019 -0800
    beginning to return data from track hub bigBed files refs #18869
  • lines changed 13, context: html, text, full: html, text
    5e4c5867d5a5b041bbaaa72dea9236c7bbb0fbf8 Tue Feb 19 14:20:38 2019 -0800
    Accidentally inserted the ENCODE section after the anniversary title section, refs #20314
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    b2391196654ee34389cc9a02d2ae390f8af607ee Mon Feb 25 09:57:37 2019 -0800
    New version number v378
• src/hg/lib/hui.c
  • lines changed 44, context: html, text, full: html, text
    bafe3eac7b6809e3e15c9171712f17ac5301c57f Fri Feb 22 14:56:22 2019 -0800
    Allow pennantIcon to be a ;-separated sequence of icon settings so we can display more than one icon next to a track name.
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    738f15cbd7318be163c5e7978bc86ccb338d4e7b Wed Feb 20 15:29:56 2019 -0800
    Adding the two new patchwork tracks to hg38, and removing the 2 old ones. Also moved a trackDb entry to a lower level to control release of altLocations track ref#18855
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    738f15cbd7318be163c5e7978bc86ccb338d4e7b Wed Feb 20 15:29:56 2019 -0800
    Adding the two new patchwork tracks to hg38, and removing the 2 old ones. Also moved a trackDb entry to a lower level to control release of altLocations track ref#18855
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 17, context: html, text, full: html, text
    738f15cbd7318be163c5e7978bc86ccb338d4e7b Wed Feb 20 15:29:56 2019 -0800
    Adding the two new patchwork tracks to hg38, and removing the 2 old ones. Also moved a trackDb entry to a lower level to control release of altLocations track ref#18855
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 19, context: html, text, full: html, text
    738f15cbd7318be163c5e7978bc86ccb338d4e7b Wed Feb 20 15:29:56 2019 -0800
    Adding the two new patchwork tracks to hg38, and removing the 2 old ones. Also moved a trackDb entry to a lower level to control release of altLocations track ref#18855
  • lines changed 10, context: html, text, full: html, text
    866ee2b1eee2321d7da87e1e6a4e62ced015d00f Thu Feb 21 09:32:11 2019 -0800
    Removing older altLocations track, new one still in hg38trackDb ref#18854
• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
  • lines changed 2, context: html, text, full: html, text
    c21cd99b2bca4866b564b0cc140ee5b42219ff4d Tue Feb 19 16:49:44 2019 -0800
    Re-enabling filter score on GH ref#22417
• src/hg/makeDb/trackDb/mouse/mm10/singleCell.html
  • lines changed 3, context: html, text, full: html, text
    aa7d0de0a26c732e26ad11db87b6b77798516f21 Wed Feb 20 15:52:02 2019 -0800
    Changing longLabels for the Tabula Muris supertrack, container, and views. refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/tabulamuris.ra
  • lines changed 5, context: html, text, full: html, text
    aa7d0de0a26c732e26ad11db87b6b77798516f21 Wed Feb 20 15:52:02 2019 -0800
    Changing longLabels for the Tabula Muris supertrack, container, and views. refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM10.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM12.html
  • lines changed 3, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM13.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM14.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM15.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM16.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM17.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM18.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM19.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM2.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM20.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM3.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM4.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM7.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM8.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM9.html
  • lines changed 2, context: html, text, full: html, text
    8cb67fc36124f34dc664a0c702a7fa362d1d6cfd Tue Feb 19 13:11:55 2019 -0800
    Updating broken links from code review. Also found some references to the wrong GENCODE release, refs #22964
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 1, context: html, text, full: html, text
    29bcc8e02433beea9995354a3127a7708c28e957 Wed Feb 20 09:19:01 2019 -0800
    editing refSeqComposite.html, refs #22659
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    17731fd83f1e8ccbfd181de1ad4f796401ae2397 Mon Feb 25 06:38:14 2019 -0800
    adding reporting guidelines to refseq docs page, refs #22970
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    738f15cbd7318be163c5e7978bc86ccb338d4e7b Wed Feb 20 15:29:56 2019 -0800
    Adding the two new patchwork tracks to hg38, and removing the 2 old ones. Also moved a trackDb entry to a lower level to control release of altLocations track ref#18855
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
  • lines changed 1, context: html, text, full: html, text
    bb46bab5cc0d54da5363d3610776b783b6dd23d4 Wed Feb 20 10:00:55 2019 -0800
    Updating redirected links for xenTro2, uiLinks cronjob.
• src/hg/makeDb/trackDb/xenTro/xenTro2/phastConsElements7way.html
  • lines changed 1, context: html, text, full: html, text
    bb46bab5cc0d54da5363d3610776b783b6dd23d4 Wed Feb 20 10:00:55 2019 -0800
    Updating redirected links for xenTro2, uiLinks cronjob.
• src/inc/common.mk
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    476cd757b51ab26fe956c287c31c19c9c1f86710 Wed Feb 20 18:19:12 2019 -0800
    correct typo error in ifneq rule no redmine
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    b2391196654ee34389cc9a02d2ae390f8af607ee Mon Feb 25 09:57:37 2019 -0800
    New version number v378
• src/lib/cheapcgi.c
  • lines changed 2, context: html, text, full: html, text
    ee3659b05d0af22a52207792b8deaf836a727fe5 Fri Feb 22 13:56:01 2019 -0800
    When hgTables gets multiple search results, hgFind calls webEnd and then hgTables needs to do cartWebEnd, so jsInlineFinish is called twice. Until the webStart/webEnd can be factored out of hgFind.c, prevent the jsInlineFinish warning from bothering the user. refs #22945
• src/utils/qa/weeklybld/buildEnv.csh
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    384e8915cf04fa4974ce3cc2e9d27c082096e7b2 Mon Feb 25 09:56:59 2019 -0800
    v378 final build, refs #22942

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• files changed: 69