All File Changes

v402_preview2 to v402_base (2020-07-27 to 2020-08-03) v402

• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    ffdee95add1181fba0699168a83223f9a228f27c Sun Aug 2 01:11:23 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/hgGene.c
  • lines changed 17, context: html, text, full: html, text
    d04a08d19a00407fb26c1abb5afa80247e84776c Wed Jul 29 15:11:32 2020 -0700
    support hgGene calls without specifying a track. Also look for default gene track if table specified is knownGene
• src/hg/hgSession/hgSession.c
  • lines changed 3, context: html, text, full: html, text
    983a9111e0930f4e3902b30390f2ee20b74513a1 Tue Jul 28 14:04:15 2020 -0700
    Remove recommended track set from cart when loading new session or changing assembly, or when panel has been closed by user click on X. refs #25601
• src/hg/hgTracks/hgTracks.c
  • lines changed 8, context: html, text, full: html, text
    983a9111e0930f4e3902b30390f2ee20b74513a1 Tue Jul 28 14:04:15 2020 -0700
    Remove recommended track set from cart when loading new session or changing assembly, or when panel has been closed by user click on X. refs #25601
  • lines changed 13, context: html, text, full: html, text
    3d25b107ddba698eee9ca53c5ea106064052eb26 Tue Jul 28 14:17:33 2020 -0700
    fix problem with config tracks changing the cart when nothing had actually changed (for Kate)
  • lines changed 5, context: html, text, full: html, text
    81a8a460976bafc57a2df88a99e47431e2258245 Fri Jul 31 11:50:52 2020 -0700
    Add hg.conf variable 'browser.recTrackSetsDetectChangge' to control whether recommended track sets features attempts to detect changes in the session. refs #25601
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    81a8a460976bafc57a2df88a99e47431e2258245 Fri Jul 31 11:50:52 2020 -0700
    Add hg.conf variable 'browser.recTrackSetsDetectChangge' to control whether recommended track sets features attempts to detect changes in the session. refs #25601
• src/hg/hgTracks/recTrackSets.c
  • lines changed 4, context: html, text, full: html, text
    983a9111e0930f4e3902b30390f2ee20b74513a1 Tue Jul 28 14:04:15 2020 -0700
    Remove recommended track set from cart when loading new session or changing assembly, or when panel has been closed by user click on X. refs #25601
  • lines changed 22, context: html, text, full: html, text
    e54c3b30f31688cffcf668d2ebacc9443f5e1743 Fri Jul 31 11:05:37 2020 -0700
    Switch to per-assembly config files for recommended track sets. refs #25601
  • lines changed 13, context: html, text, full: html, text
    81a8a460976bafc57a2df88a99e47431e2258245 Fri Jul 31 11:50:52 2020 -0700
    Add hg.conf variable 'browser.recTrackSetsDetectChangge' to control whether recommended track sets features attempts to detect changes in the session. refs #25601
• src/hg/hgTracks/vcfTrack.c
  • lines changed 130, context: html, text, full: html, text
    be693595e590bce1d7d9b5e0d34451047c3170f2 Thu Jul 30 15:52:52 2020 -0700
    Add 2 new color options for trios, color by predicted functional affect and de novo child variants, refs #25983
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    fbe9bce3a858f2ed909fdeeddde3191efbd33163 Tue Jul 28 13:04:02 2020 -0700
    reference kgXref from the default knownGene database
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 5, context: html, text, full: html, text
    63bd069141e86d8b02dca271e55b2cdb25245522 Tue Jul 28 16:51:56 2020 -0700
    added SARS-CoV-2 to release log. updated blurb abt chrMT
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 47, context: html, text, full: html, text
    4c4f8c1575f52b1e256fb6c4d4a318d2eee2b526 Mon Jul 27 14:59:34 2020 -0700
    adding new video and announcing
  • lines changed 3, context: html, text, full: html, text
    cdafb1cf13c83e2364863e2fc2322eb1d7dcefd9 Mon Jul 27 15:12:15 2020 -0700
    adding to description of what's in new video
• src/hg/htdocs/inc/recTrackSets.hg19.tab
  • lines changed 11, context: html, text, full: html, text
    47a3a952b4c984d38454843fc638e6ea2ebbdfe8 Fri Jul 31 11:07:06 2020 -0700
    Switch to per-assembly config files for recommended track sets. refs #25601
• src/hg/htdocs/inc/recommendedTrackSets.tab
  • lines changed 11, context: html, text, full: html, text
    47a3a952b4c984d38454843fc638e6ea2ebbdfe8 Fri Jul 31 11:07:06 2020 -0700
    Switch to per-assembly config files for recommended track sets. refs #25601
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    4c4f8c1575f52b1e256fb6c4d4a318d2eee2b526 Mon Jul 27 14:59:34 2020 -0700
    adding new video and announcing
• src/hg/htdocs/training/index.html
  • lines changed 22, context: html, text, full: html, text
    4c4f8c1575f52b1e256fb6c4d4a318d2eee2b526 Mon Jul 27 14:59:34 2020 -0700
    adding new video and announcing
• src/hg/inc/cart.h
  • lines changed 1, context: html, text, full: html, text
    983a9111e0930f4e3902b30390f2ee20b74513a1 Tue Jul 28 14:04:15 2020 -0700
    Remove recommended track set from cart when loading new session or changing assembly, or when panel has been closed by user click on X. refs #25601
• src/hg/inc/vcfUi.h
  • lines changed 7, context: html, text, full: html, text
    be693595e590bce1d7d9b5e0d34451047c3170f2 Thu Jul 30 15:52:52 2020 -0700
    Add 2 new color options for trios, color by predicted functional affect and de novo child variants, refs #25983
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    b78d3ab17bc388d13818cf1afa834692968a608c Mon Aug 3 10:00:27 2020 -0700
    New version number v402
• src/hg/js/hgTracks.js
  • lines changed 7, context: html, text, full: html, text
    e63ad6b1e67c7e2acf3c1bb5eb493f4dc8ef9217 Mon Jul 27 13:57:24 2020 -0700
    Temp fix for hang on hide all plus turn on track. refs #25601
  • lines changed 7, context: html, text, full: html, text
    ad817e42579bdda050549af9f5a9f9813453d83f Tue Jul 28 12:17:53 2020 -0700
    Restore mouseover change when track set changes, fixing prob with undefined object. TODO is to short-circuit updateSessionPanel when no rec track set. refs #25601
  • lines changed 1, context: html, text, full: html, text
    983a9111e0930f4e3902b30390f2ee20b74513a1 Tue Jul 28 14:04:15 2020 -0700
    Remove recommended track set from cart when loading new session or changing assembly, or when panel has been closed by user click on X. refs #25601
  • lines changed 3, context: html, text, full: html, text
    29bc20158ae8382d65736b149da8071d1f4cfd76 Fri Jul 31 09:40:54 2020 -0700
    Update position properly in track set link. refs #25601
  • lines changed 35, context: html, text, full: html, text
    81a8a460976bafc57a2df88a99e47431e2258245 Fri Jul 31 11:50:52 2020 -0700
    Add hg.conf variable 'browser.recTrackSetsDetectChangge' to control whether recommended track sets features attempts to detect changes in the session. refs #25601
• src/hg/lib/customFactory.c
  • lines changed 0, context: html, text, full: html, text
    8d6ffe3600666762eb0145c4fead9883d77273c0 Tue Jul 28 15:11:53 2020 -0700
    Adding a missing trailing space on an error message see update4 in refs #25891
• src/hg/lib/hgFind.c
  • lines changed 2, context: html, text, full: html, text
    0da816d620bff2bb12b290492603ec5a8d17238d Tue Jul 28 14:40:58 2020 -0700
    fix singleSearch to use default gene set
  • lines changed 3, context: html, text, full: html, text
    e9f355b6e52871d26cd5a84177d7abb3297316fa Tue Jul 28 15:08:06 2020 -0700
    oops... another tweak to support singleSearch
• src/hg/lib/vcfUi.c
  • lines changed 22, context: html, text, full: html, text
    be693595e590bce1d7d9b5e0d34451047c3170f2 Thu Jul 30 15:52:52 2020 -0700
    Add 2 new color options for trios, color by predicted functional affect and de novo child variants, refs #25983
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 17, context: html, text, full: html, text
    c6768809fed768591851aa1547d1f5e867727a2f Wed Jul 29 12:41:26 2020 -0700
    liftOvers from canFam5 to Fam3 Fam4 and vs. vs. refs #25917
• src/hg/makeDb/doc/canFam4/initialBuild.txt
  • lines changed 19, context: html, text, full: html, text
    c6768809fed768591851aa1547d1f5e867727a2f Wed Jul 29 12:41:26 2020 -0700
    liftOvers from canFam5 to Fam3 Fam4 and vs. vs. refs #25917
• src/hg/makeDb/doc/canFam5/initialBuild.txt
  • lines changed 131, context: html, text, full: html, text
    c6768809fed768591851aa1547d1f5e867727a2f Wed Jul 29 12:41:26 2020 -0700
    liftOvers from canFam5 to Fam3 Fam4 and vs. vs. refs #25917
• src/hg/makeDb/doc/gorGor6/initialBuild.txt
  • lines changed 164, context: html, text, full: html, text
    b4c1647f1ae2f77b8657427712609730a9da81fa Tue Jul 28 11:15:01 2020 -0700
    done and in pushQ refs #24524
• src/hg/makeDb/doc/mm10.txt
  • lines changed 89, context: html, text, full: html, text
    f6bb7fb8b0af020a2d602824f74d84d516bd96fb Thu Jul 30 15:12:36 2020 -0700
    liftOver mm10 to mm39 to mm10 completed refs #22271
• src/hg/makeDb/doc/mm39/initialBuild.txt
  • lines changed 1199, context: html, text, full: html, text
    c6142e28bc43936027fcfa20acdea1cbf6b99209 Mon Jul 27 15:27:42 2020 -0700
    begin build of mm39 refs #22271
  • lines changed 292, context: html, text, full: html, text
    f6bb7fb8b0af020a2d602824f74d84d516bd96fb Thu Jul 30 15:12:36 2020 -0700
    liftOver mm10 to mm39 to mm10 completed refs #22271
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV35.sh
  • lines changed 42, context: html, text, full: html, text
    a3411a622fcf54100e80fd388cbda49afed17612 Mon Aug 3 09:31:04 2020 -0700
    ongoing work on merged gene set
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    087aaa0dd2c433c5da4280b808759aca82695634 Wed Jul 29 13:37:45 2020 -0700
    Added canFam5 - dog refs #25917
  • lines changed 1, context: html, text, full: html, text
    0dbf36fe5ceb398640c5fa2b64022bcbe4d2147e Thu Jul 30 10:05:25 2020 -0700
    Added mm39 - mouse refs #22271
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 18, context: html, text, full: html, text
    8d2d04a5414fc413cdf188edfa3e9ee26a597d79 Wed Jul 29 13:36:49 2020 -0700
    Added canFam5 dog; refs #25917
  • lines changed 20, context: html, text, full: html, text
    ba89366e6b1e0c1eb357a9d67bf978fa59612ffc Thu Jul 30 10:04:35 2020 -0700
    Added mm39 mouse; refs #22271
  • lines changed 1, context: html, text, full: html, text
    b4dc79691dba0b82c4253ce9bc9baeb1ce2156fe Fri Jul 31 12:37:27 2020 -0700
    Added canFam5 dog; refs #25917
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    087aaa0dd2c433c5da4280b808759aca82695634 Wed Jul 29 13:37:45 2020 -0700
    Added canFam5 - dog refs #25917
  • lines changed 1, context: html, text, full: html, text
    0dbf36fe5ceb398640c5fa2b64022bcbe4d2147e Thu Jul 30 10:05:25 2020 -0700
    Added mm39 - mouse refs #22271
• src/hg/makeDb/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    52b68e67791a212a38b70eb97d16cbd946d5631f Wed Jul 29 13:41:15 2020 -0700
    adding rules for canFam5 refs #25917
  • lines changed 11, context: html, text, full: html, text
    74c7146bcbc72e8ab3c719d2edd4ec53c25f21ae Thu Jul 30 10:24:14 2020 -0700
    adding rules for mm39 refs #22271
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 1, context: html, text, full: html, text
    ebc68f5e6151d7f361887c0027bb4cd8776c277e Mon Jul 27 12:11:37 2020 -0700
    fixing typo in last fix
• src/hg/makeDb/trackDb/human/hg38/omimGene2.html
  • lines changed 44, context: html, text, full: html, text
    387f39bbf46e7335af8a772bbfb63782df784de7 Fri Jul 31 12:56:45 2020 -0700
    Adding data access to OMIM refs #18419
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    be693595e590bce1d7d9b5e0d34451047c3170f2 Thu Jul 30 15:52:52 2020 -0700
    Add 2 new color options for trios, color by predicted functional affect and de novo child variants, refs #25983
• src/hg/makeDb/trackDb/human/lovdComp.html
  • lines changed 1, context: html, text, full: html, text
    174335dd9f478a729210e2fd7debddfae82e75dc Mon Jul 27 15:19:06 2020 -0700
    corrected long variant cutt off in the long track name and description page, no redmine
• src/hg/makeDb/trackDb/human/omimGene2.html
  • lines changed 43, context: html, text, full: html, text
    cfe373a8c5d27a4cdac6ce39b2a50f5cf4e63948 Fri Jul 31 14:11:36 2020 -0700
    Adding Data Access and example for OMIM refs #18419
  • lines changed 1, context: html, text, full: html, text
    8e22e6e2afe9bb9df058ba48430a679702e79391 Fri Jul 31 15:22:29 2020 -0700
    Minor type fix #18419
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 22, context: html, text, full: html, text
    4bd3913b145415c4d24d5c6b2fa9ee5b966257c5 Fri Jul 31 11:44:52 2020 -0700
    More clinGen dosage changes after extrernal feedback, refs #24818
  • lines changed 2, context: html, text, full: html, text
    cfabc62e560b5917402da1e6d6414ba588a5367d Fri Jul 31 12:37:00 2020 -0700
    Add omim phenotypes to clinGen dosage tracks, refs #24818
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    174335dd9f478a729210e2fd7debddfae82e75dc Mon Jul 27 15:19:06 2020 -0700
    corrected long variant cutt off in the long track name and description page, no redmine
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    6d3777492e0787c25dee9d0dfe52c7585ee1382b Mon Jul 27 13:04:13 2020 -0700
    adding mm39 to the browser refs #22271
• src/hg/makeDb/trackDb/mouse/mm39/description.html
  • lines changed 63, context: html, text, full: html, text
    6d3777492e0787c25dee9d0dfe52c7585ee1382b Mon Jul 27 13:04:13 2020 -0700
    adding mm39 to the browser refs #22271
• src/hg/makeDb/trackDb/mouse/mm39/gap.html
  • lines changed 34, context: html, text, full: html, text
    6d3777492e0787c25dee9d0dfe52c7585ee1382b Mon Jul 27 13:04:13 2020 -0700
    adding mm39 to the browser refs #22271
• src/hg/makeDb/trackDb/mouse/mm39/gold.html
  • lines changed 37, context: html, text, full: html, text
    6d3777492e0787c25dee9d0dfe52c7585ee1382b Mon Jul 27 13:04:13 2020 -0700
    adding mm39 to the browser refs #22271
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    6d3777492e0787c25dee9d0dfe52c7585ee1382b Mon Jul 27 13:04:13 2020 -0700
    adding mm39 to the browser refs #22271
  • lines changed 6, context: html, text, full: html, text
    a7986965ab5a0778cc4784339c5250eb55deaa61 Mon Jul 27 16:04:02 2020 -0700
    adding search rule for gold/assembly track refs #22271
  • lines changed 1, context: html, text, full: html, text
    a3c6c2219eb01d33cb88b8a58c7e8db9606191b2 Fri Jul 31 13:17:49 2020 -0700
    try out a xenoRefGene track refs #22271
• src/hg/makeDb/trackDb/mouse/mm39/xenoRefGene.html
  • lines changed 90, context: html, text, full: html, text
    a3c6c2219eb01d33cb88b8a58c7e8db9606191b2 Fri Jul 31 13:17:49 2020 -0700
    try out a xenoRefGene track refs #22271
  • lines changed 1, context: html, text, full: html, text
    d777e352913f691aaa106669ed4a6e660e8ea6e4 Fri Jul 31 13:19:41 2020 -0700
    try out a xenoRefGene track refs #22271
• src/hg/makeDb/trackDb/mouse/mm39/xenoRefGene.ra
  • lines changed 12, context: html, text, full: html, text
    a3c6c2219eb01d33cb88b8a58c7e8db9606191b2 Fri Jul 31 13:17:49 2020 -0700
    try out a xenoRefGene track refs #22271
  • lines changed 1, context: html, text, full: html, text
    d8d08237bc1285af4c37bb0ca0ce402db95a950d Fri Jul 31 13:46:04 2020 -0700
    can not use the track name xenoRefGene refs #22271
• src/hg/makeDb/trackDb/rhesus/rheMac10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    663ba8d8330dba3c7062780df90d243c996453a2 Fri Jul 31 13:28:17 2020 -0700
    Adding pennantIcon to new track refs #25602
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    be693595e590bce1d7d9b5e0d34451047c3170f2 Thu Jul 30 15:52:52 2020 -0700
    Add 2 new color options for trios, color by predicted functional affect and de novo child variants, refs #25983
• src/hg/makeDb/trackDb/virus/wuhCor1/contacts.html
  • lines changed 1, context: html, text, full: html, text
    0fb281f887c665ecd86d040490f83b3e5006db8f Mon Jul 27 15:01:26 2020 -0700
    Small grammar fix refs #25910
• src/hg/makeDb/trackDb/virus/wuhCor1/phyloGenes.html
  • lines changed 24, context: html, text, full: html, text
    2d15787622b884307215877e2e18daae1559509b Mon Jul 27 15:49:07 2020 -0700
    Adding data access section to new track refs #25946
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    5ed1b9472675a26c2584f63345e913b22ff0e27f Mon Jul 27 13:20:30 2020 -0700
    Adding group to the genes track refs #25946
  • lines changed 2, context: html, text, full: html, text
    d37025aa5b81c4c4d945352fe142e5d26bc10b6c Tue Jul 28 14:02:03 2020 -0700
    Adding pennantIcons for new tracks refs #10138 #25946
  • lines changed 1, context: html, text, full: html, text
    029fb92ec0f20c40e121e7cba1d8b2eedc253e77 Tue Jul 28 14:17:36 2020 -0700
    Setting default vis to hide refs #25910
  • lines changed 3, context: html, text, full: html, text
    d52959d88bc364406e5a832494b0ab9ca923e965 Tue Jul 28 17:24:09 2020 -0700
    Prep release for prob regions #25916
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 9, context: html, text, full: html, text
    e46c2148e1d280975b160ad98202d6ea4a2739ab Fri Jul 31 15:40:54 2020 -0700
    added ability to pass through parasol -priority option doBlastzChainNet.pl and probably all HgAutomate stuff. Keep us bottom feeders where we belong
• src/hg/utils/otto/clinGen/makeDosage.sh
  • lines changed 14, context: html, text, full: html, text
    4bd3913b145415c4d24d5c6b2fa9ee5b966257c5 Fri Jul 31 11:44:52 2020 -0700
    More clinGen dosage changes after extrernal feedback, refs #24818
  • lines changed 29, context: html, text, full: html, text
    cfabc62e560b5917402da1e6d6414ba588a5367d Fri Jul 31 12:37:00 2020 -0700
    Add omim phenotypes to clinGen dosage tracks, refs #24818
• src/hg/utils/otto/clinGen/processClinGenDosage.py
  • lines changed 202, context: html, text, full: html, text
    4bd3913b145415c4d24d5c6b2fa9ee5b966257c5 Fri Jul 31 11:44:52 2020 -0700
    More clinGen dosage changes after extrernal feedback, refs #24818
  • lines changed 31, context: html, text, full: html, text
    cfabc62e560b5917402da1e6d6414ba588a5367d Fri Jul 31 12:37:00 2020 -0700
    Add omim phenotypes to clinGen dosage tracks, refs #24818
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    b78d3ab17bc388d13818cf1afa834692968a608c Mon Aug 3 10:00:27 2020 -0700
    New version number v402
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    aac5e20f60c4cc77534a62c05f646b033574680b Mon Aug 3 09:49:07 2020 -0700
    v402 final build

• lines changed: 3133
• files changed: 83