All File Changes

v396_preview to v396_preview2 (2020-03-16 to 2020-03-23) v396

• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 135, context: html, text, full: html, text
    ea1508d83bb99583cb9ec1ff630b938187a44006 Tue Nov 26 08:13:06 2019 -0800
    Change 'validate hub' to 'Hub Development' and display custom help explaining that this tab is for running hubCheck. Also add a button to load the hub on hgTracks, and a dropdown with extra checkboxes for turning on udcTimeout and measureTiming. refs #24599
  • lines changed 1, context: html, text, full: html, text
    a84eb84eb5342a776e9c98f1914cd73fb5e08cb5 Tue Mar 17 14:57:38 2020 -0700
    Fixing typo in help text for udcTimeout option on hub validate page, refs #24559
  • lines changed 12, context: html, text, full: html, text
    9786016a1473b5a4f97283db2cf34a092e0085c1 Wed Mar 18 09:25:39 2020 -0700
    Add udcTimout and measureTiming to validate form to save the checkbox selections for after checking the hub, pointed out by Dan, refs #24559
  • lines changed 1, context: html, text, full: html, text
    a5bc9c34399b3646a0d8e077fe2b6ed0f6ed0c44 Wed Mar 18 09:52:15 2020 -0700
    Fixing broken redirect from hgHubConnect to hgTracks, refs #24559
  • lines changed 2, context: html, text, full: html, text
    26a2f2cccdb04a9b1b54487ae74fd2c1c2b611d4 Wed Mar 18 13:13:51 2020 -0700
    Making more clear what the advanced features of the hub development tab are for, refs #24559
• src/hg/hgTracks/vcfTrack.c
  • lines changed 44, context: html, text, full: html, text
    5c8f8925eb335bb375595e839368c3f7594ea7e4 Mon Mar 16 12:24:10 2020 -0700
    Libify code that counts genotypes correctly from vcfClick.c and use it in vcfTrack.c. refs #24623, fixes #25165
  • lines changed 134, context: html, text, full: html, text
    42d91822ec103cfcc74e9f69b39d3ad8d886c278 Wed Mar 18 15:25:15 2020 -0700
    Add a new trackDb setting hapClusterMethod and corresponding UI option for drawing haplotypes in VCF file order instead of clustering. refs #25197 Applied the new setting to mm10 strainSNPs and increased its default height so that strain labels appear in the left label area.
• src/hg/hgc/vcfClick.c
  • lines changed 58, context: html, text, full: html, text
    5c8f8925eb335bb375595e839368c3f7594ea7e4 Mon Mar 16 12:24:10 2020 -0700
    Libify code that counts genotypes correctly from vcfClick.c and use it in vcfTrack.c. refs #24623, fixes #25165
  • lines changed 11, context: html, text, full: html, text
    42d91822ec103cfcc74e9f69b39d3ad8d886c278 Wed Mar 18 15:25:15 2020 -0700
    Add a new trackDb setting hapClusterMethod and corresponding UI option for drawing haplotypes in VCF file order instead of clustering. refs #25197 Applied the new setting to mm10 strainSNPs and increased its default height so that strain labels appear in the left label area.
• src/hg/htdocs/covid19/covid.css
  • lines changed 47, context: html, text, full: html, text
    701d97e546b188346f35aced8bd2661279eb5a5b Sat Mar 21 07:22:11 2020 -0700
    adding covid css
• src/hg/htdocs/covid19/index.html
  • lines changed 292, context: html, text, full: html, text
    46993f5d2f87efc87bdd533ccbf05ae98d0142f3 Sat Mar 21 07:19:46 2020 -0700
    adding covid page
  • lines changed 154, context: html, text, full: html, text
    4b5c55170859286c0204cffcf647ac2d1ae886a2 Sat Mar 21 08:04:24 2020 -0700
    covid19 index page
  • lines changed 76, context: html, text, full: html, text
    42126a0ec22129f21585d3a47e27f5c494fdd6c2 Mon Mar 23 09:50:09 2020 -0700
    covid 19 landing page, refs #25217
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    eafe9e9c996090afb29d8dd2e90ec2fb9e181632 Wed Mar 18 13:10:45 2020 -0700
    Fixing some inconsistencies in the trackDb defnition doc for hideEmptySubtracks, no RM
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 29, context: html, text, full: html, text
    92bf9b755b6bcaf3c69c3332f5e42ce53ec3555f Tue Mar 17 16:55:38 2020 -0700
    Announcing the chrMT patch, refs #24648
• src/hg/htdocs/images/covid19-transmission.mar2020.nextstrain.png
  • lines changed 0, context: html, text, full: html, text
    f3a4f806a45ccbf88850ce5b3370ddc79e80390b Thu Mar 19 14:29:59 2020 -0700
    Supporting files for updated SARS-2 assembly description. refs #25185
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    92bf9b755b6bcaf3c69c3332f5e42ce53ec3555f Tue Mar 17 16:55:38 2020 -0700
    Announcing the chrMT patch, refs #24648
• src/hg/htdocs/style/hgHubConnect.css
  • lines changed 66, context: html, text, full: html, text
    ea1508d83bb99583cb9ec1ff630b938187a44006 Tue Nov 26 08:13:06 2019 -0800
    Change 'validate hub' to 'Hub Development' and display custom help explaining that this tab is for running hubCheck. Also add a button to load the hub on hgTracks, and a dropdown with extra checkboxes for turning on udcTimeout and measureTiming. refs #24599
• src/hg/htdocs/training/index.html
  • lines changed 38, context: html, text, full: html, text
    a8318a63efcaccbe334b8d8ef2bdebbda3e7e882 Fri Mar 20 11:44:22 2020 -0700
    removed passed, but cancelled portland and acmd workshops. added cancelled to piran and iasi. added links to coronavirus
• src/hg/inc/hubConnect.h
  • lines changed 1, context: html, text, full: html, text
    ea1508d83bb99583cb9ec1ff630b938187a44006 Tue Nov 26 08:13:06 2019 -0800
    Change 'validate hub' to 'Hub Development' and display custom help explaining that this tab is for running hubCheck. Also add a button to load the hub on hgTracks, and a dropdown with extra checkboxes for turning on udcTimeout and measureTiming. refs #24599
• src/hg/inc/vcfUi.h
  • lines changed 4, context: html, text, full: html, text
    42d91822ec103cfcc74e9f69b39d3ad8d886c278 Wed Mar 18 15:25:15 2020 -0700
    Add a new trackDb setting hapClusterMethod and corresponding UI option for drawing haplotypes in VCF file order instead of clustering. refs #25197 Applied the new setting to mm10 strainSNPs and increased its default height so that strain labels appear in the left label area.
• src/hg/js/dbDbTaxonomy.js
  • lines changed 1, context: html, text, full: html, text
    f3a4f806a45ccbf88850ce5b3370ddc79e80390b Thu Mar 19 14:29:59 2020 -0700
    Supporting files for updated SARS-2 assembly description. refs #25185
• src/hg/js/hgHubConnect.js
  • lines changed 6, context: html, text, full: html, text
    ea1508d83bb99583cb9ec1ff630b938187a44006 Tue Nov 26 08:13:06 2019 -0800
    Change 'validate hub' to 'Hub Development' and display custom help explaining that this tab is for running hubCheck. Also add a button to load the hub on hgTracks, and a dropdown with extra checkboxes for turning on udcTimeout and measureTiming. refs #24599
• src/hg/lib/vcfUi.c
  • lines changed 32, context: html, text, full: html, text
    42d91822ec103cfcc74e9f69b39d3ad8d886c278 Wed Mar 18 15:25:15 2020 -0700
    Add a new trackDb setting hapClusterMethod and corresponding UI option for drawing haplotypes in VCF file order instead of clustering. refs #25197 Applied the new setting to mm10 strainSNPs and increased its default height so that strain labels appear in the left label area.
• src/hg/makeDb/doc/assemblyEquivalence/README.txt
  • lines changed 147, context: html, text, full: html, text
    caa7d37fe23e92494b9c694c2e91c8d98e3a846c Thu Mar 19 12:51:40 2020 -0700
    document the procedure refs #24547
• src/hg/makeDb/doc/danRer10/lastzRuns.txt
  • lines changed 222, context: html, text, full: html, text
    6091558bab452de0ba020f3e08a9d20ef9aa3d81 Wed Mar 18 19:09:58 2020 -0700
    lastz runs for 12-way alignment on danRer10 per research request no redmine
• src/hg/makeDb/doc/danRer10/multiz12way.txt
  • lines changed 1547, context: html, text, full: html, text
    1a0f4d5f930cae12004cec43fbb0cc6f34774651 Wed Mar 18 16:23:38 2020 -0700
    12-way alignment on danRer10 per researcher request to redmine
• src/hg/makeDb/doc/galGal6/lastzRuns.txt
  • lines changed 73, context: html, text, full: html, text
    6091558bab452de0ba020f3e08a9d20ef9aa3d81 Wed Mar 18 19:09:58 2020 -0700
    lastz runs for 12-way alignment on danRer10 per research request no redmine
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 35, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/doc/mm10.txt
  • lines changed 33, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes20.sh
  • lines changed 8, context: html, text, full: html, text
    b63c6cd3032d2395c889cb0a58b28464d9d7f6a6 Tue Mar 17 09:01:34 2020 -0700
    fix some of the problems from #25160
• src/hg/makeDb/doc/wuhCor1/initialBuild.txt
  • lines changed 5, context: html, text, full: html, text
    d7a0a8fc6582a80932f8ac14edfaefc988d08963 Tue Mar 17 09:24:16 2020 -0700
    defaultPosition reset to whole sequence refs #24851
  • lines changed 9, context: html, text, full: html, text
    0e7af05897ea135e3a3be9e5ae0451fabea80769 Tue Mar 17 15:17:15 2020 -0700
    made ncbiGene into a bigGenePred. Added fields for uniProt gene name and uniProt description
  • lines changed 3, context: html, text, full: html, text
    ed72e3ea2e125d40211407d568a5daac06466d2e Fri Mar 20 17:04:39 2020 -0700
    Adding makeDb/doc note about Nexstrain tracks (otto) - refs #25188
• src/hg/makeDb/doc/wuhCor1/multiz44.txt
  • lines changed 122, context: html, text, full: html, text
    f20d7975d0373acb690ba6df158ed9a39786f9a1 Wed Mar 18 11:44:06 2020 -0700
    finished with 44-way track refs #25187
• src/hg/makeDb/doc/wuhCor1/phastCons119way.txt
  • lines changed 4, context: html, text, full: html, text
    b05f926380653f4581aabe1521ff12799f244925 Thu Mar 19 14:22:56 2020 -0700
    fix dates on DONE statements refs #25187
• src/hg/makeDb/doc/wuhCor1/phastCons44way.txt
  • lines changed 13, context: html, text, full: html, text
    f20d7975d0373acb690ba6df158ed9a39786f9a1 Wed Mar 18 11:44:06 2020 -0700
    finished with 44-way track refs #25187
  • lines changed 4, context: html, text, full: html, text
    b05f926380653f4581aabe1521ff12799f244925 Thu Mar 19 14:22:56 2020 -0700
    fix dates on DONE statements refs #25187
• src/hg/makeDb/doc/wuhCor1/snpView.44way.txt
  • lines changed 11, context: html, text, full: html, text
    f20d7975d0373acb690ba6df158ed9a39786f9a1 Wed Mar 18 11:44:06 2020 -0700
    finished with 44-way track refs #25187
• src/hg/makeDb/doc/xenTro9/lastzRuns.txt
  • lines changed 67, context: html, text, full: html, text
    6091558bab452de0ba020f3e08a9d20ef9aa3d81 Wed Mar 18 19:09:58 2020 -0700
    lastz runs for 12-way alignment on danRer10 per research request no redmine
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 10, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/schema/all.joiner
  • lines changed 15, context: html, text, full: html, text
    bac632e3041cdfd281733475e9429cb283266e6c Fri Mar 20 08:19:19 2020 -0700
    adding tablesIgnored for wuhCor1 refs #25187
  • lines changed 194, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 4, context: html, text, full: html, text
    fba9c628e3856b0905177b738588ae0ff0e64c7b Wed Mar 18 13:16:25 2020 -0700
    Removing release tags on hg19 gnomAD pLI score track refs #20394
  • lines changed 4, context: html, text, full: html, text
    13b24016a7d8b3e91fdeebd7ee925916a8b96baf Wed Mar 18 15:24:34 2020 -0700
    Fixing default visibilities refs #20394
  • lines changed 1, context: html, text, full: html, text
    b386f6f58a9091259e0e6afe559c6c49a8491fb3 Wed Mar 18 15:54:28 2020 -0700
    Fixing default visibilities refs #20394
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV34.html
  • lines changed 47, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV34.ra
  • lines changed 286, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    42d91822ec103cfcc74e9f69b39d3ad8d886c278 Wed Mar 18 15:25:15 2020 -0700
    Add a new trackDb setting hapClusterMethod and corresponding UI option for drawing haplotypes in VCF file order instead of clustering. refs #25197 Applied the new setting to mm10 strainSNPs and increased its default height so that strain labels appear in the left label area.
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM25.html
  • lines changed 30, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM25.ra
  • lines changed 286, context: html, text, full: html, text
    db0877a0f789518c170e95923feee7ad95e15b55 Sun Mar 22 09:14:47 2020 -0700
    import of GENCODE V34 and VM25 prereleases
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    fbf5542d502a7075b811b9efc9fe6c158630aa61 Wed Mar 18 08:23:07 2020 -0700
    allowing exonNumbers off for bigGenePred.
  • lines changed 1, context: html, text, full: html, text
    42d91822ec103cfcc74e9f69b39d3ad8d886c278 Wed Mar 18 15:25:15 2020 -0700
    Add a new trackDb setting hapClusterMethod and corresponding UI option for drawing haplotypes in VCF file order instead of clustering. refs #25197 Applied the new setting to mm10 strainSNPs and increased its default height so that strain labels appear in the left label area.
• src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html
  • lines changed 24, context: html, text, full: html, text
    df0cd0f673fc986780f2ce78ae2b32803720f79b Mon Mar 16 15:22:01 2020 -0700
    small corrections to text refs #25090
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    89e09c560ebabadc38bc1bd9fa70fcfb4e23e8d5 Wed Mar 18 08:06:52 2020 -0700
    adding details about 119 and 44 way conservation tracks, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/cons44way.html
  • lines changed 443, context: html, text, full: html, text
    e0474e610833d8e58cc5c828b9bc99bc0e536444 Mon Mar 16 15:18:50 2020 -0700
    add 44-way description page refs #25090
  • lines changed 1, context: html, text, full: html, text
    df0cd0f673fc986780f2ce78ae2b32803720f79b Mon Mar 16 15:22:01 2020 -0700
    small corrections to text refs #25090
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    59bfcd59f58c21c2c778ab0ef11d58e237b66312 Fri Mar 20 13:23:46 2020 -0700
    Fixing a typo in goldenPath for a download file, refs #25187
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
  • lines changed 49, context: html, text, full: html, text
    9b49db94c17cbcc3aaf92d39b08d52c348a9f2bc Thu Mar 19 13:19:44 2020 -0700
    First pass of hand-work on SARS-2 description. Add intro and remove uselss search section. refs #25185
  • lines changed 42, context: html, text, full: html, text
    1ad701bb29765bca98c1775e15cb1c016eacc6dd Thu Mar 19 14:25:43 2020 -0700
    Add links and transmission graphic from nextstrain.org. Ready for review. refs #25185
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    38a438f73041b5d7edf7a5740814fc3ee2096daf Fri Mar 20 12:00:09 2020 -0700
    Work around layout problem on older Safari's. refs #25185
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.html
  • lines changed 9, context: html, text, full: html, text
    cbb07b120b71d7e6357a8224342e2d4ac4635ab5 Tue Mar 17 09:02:40 2020 -0700
    updating cov2 epitopes track, no redmine
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    8d4a8ad80c87296491883750999e9ece571cdd03 Mon Mar 23 02:27:58 2020 -0700
    changes after david H QA, refs #25190
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.ra
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    7502a793d1219ff6be9741878055eb873d565d9e Mon Mar 16 10:20:33 2020 -0700
    correct track type bigBed 9 + not bigBed 9+ refs #25090
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    cbb07b120b71d7e6357a8224342e2d4ac4635ab5 Tue Mar 17 09:02:40 2020 -0700
    updating cov2 epitopes track, no redmine
  • lines changed 2, context: html, text, full: html, text
    024fff8aa011bb0300e20776ad95e486c5eeec62 Thu Mar 19 08:45:54 2020 -0700
    Fixing up uniprot track trackDbs for wuhCor1,refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGene.html
  • lines changed 19, context: html, text, full: html, text
    0e7af05897ea135e3a3be9e5ae0451fabea80769 Tue Mar 17 15:17:15 2020 -0700
    made ncbiGene into a bigGenePred. Added fields for uniProt gene name and uniProt description
  • lines changed 19, context: html, text, full: html, text
    262feb6d94b84b2d407cf1454dc1e49b6e865da9 Fri Mar 20 12:07:25 2020 -0700
    new NCBI genes on dev only for the moment
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGene.ra
  • lines changed 15, context: html, text, full: html, text
    262feb6d94b84b2d407cf1454dc1e49b6e865da9 Fri Mar 20 12:07:25 2020 -0700
    new NCBI genes on dev only for the moment
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.html
  • lines changed 19, context: html, text, full: html, text
    0e7af05897ea135e3a3be9e5ae0451fabea80769 Tue Mar 17 15:17:15 2020 -0700
    made ncbiGene into a bigGenePred. Added fields for uniProt gene name and uniProt description
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.ra
  • lines changed 15, context: html, text, full: html, text
    262feb6d94b84b2d407cf1454dc1e49b6e865da9 Fri Mar 20 12:07:25 2020 -0700
    new NCBI genes on dev only for the moment
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClades.html
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    e31031d4e2c16bf5cdaa714622babba23c15976e Sat Mar 21 08:54:14 2020 -0700
    first go at nextstrain docs pages, refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainGene.html
  • lines changed 29, context: html, text, full: html, text
    e31031d4e2c16bf5cdaa714622babba23c15976e Sat Mar 21 08:54:14 2020 -0700
    first go at nextstrain docs pages, refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainVars.html
  • lines changed 66, context: html, text, full: html, text
    e31031d4e2c16bf5cdaa714622babba23c15976e Sat Mar 21 08:54:14 2020 -0700
    first go at nextstrain docs pages, refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/primers.html
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    31981b419fbc5f2dd4651e1c8f8dba1457bc97c3 Tue Mar 17 06:47:04 2020 -0700
    adding primers track to cov2, no redmine, email from Jason
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra
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    92fc3abf1b0a613ebc3160bfb07a906166081eac Wed Mar 18 08:29:27 2020 -0700
    fixing 119 strains labels, refs #25090
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    e9ce785f1c0baf2a04c9ee6f3e2d7f9f5b65b3af Wed Mar 18 08:38:27 2020 -0700
    small change to 119 track label
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    879041dca6623320be63dbcbfceaf82dec2bd49a Wed Mar 18 09:24:41 2020 -0700
    update default visibility refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.44way.ra
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    89e09c560ebabadc38bc1bd9fa70fcfb4e23e8d5 Wed Mar 18 08:06:52 2020 -0700
    adding details about 119 and 44 way conservation tracks, refs #25090
  • lines changed 1, context: html, text, full: html, text
    92fc3abf1b0a613ebc3160bfb07a906166081eac Wed Mar 18 08:29:27 2020 -0700
    fixing 119 strains labels, refs #25090
  • lines changed 2, context: html, text, full: html, text
    879041dca6623320be63dbcbfceaf82dec2bd49a Wed Mar 18 09:24:41 2020 -0700
    update default visibility refs #25090
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    3b9f2d1f1cd5cd0865999babd3563e38d78d224e Thu Mar 19 09:48:34 2020 -0700
    changing long label of bat alignment track, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
  • lines changed 29, context: html, text, full: html, text
    fd95861dbf3dd970c833b11076daa0da8738b1e8 Fri Mar 20 16:43:31 2020 -0700
    Adding 3 tracks derived from nextstrain.org: Nextstrain {Genes, Clades, Variants}. refs #25188
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    720ff382be5d9492be9a896896185469f87de003 Fri Mar 20 17:01:33 2020 -0700
    Bump up priority of coronavirus Nextstrain tracks so they appear before RepeatMasker which doesn't really apply to viruses. refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    31981b419fbc5f2dd4651e1c8f8dba1457bc97c3 Tue Mar 17 06:47:04 2020 -0700
    adding primers track to cov2, no redmine, email from Jason
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    fa8c37b486373445a92f0c2fe9e50c4442bca8e3 Tue Mar 17 09:16:25 2020 -0700
    setting gap and rmsk to hide, adding uniprot as a default track, email from Mark
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    0e7af05897ea135e3a3be9e5ae0451fabea80769 Tue Mar 17 15:17:15 2020 -0700
    made ncbiGene into a bigGenePred. Added fields for uniProt gene name and uniProt description
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    89e09c560ebabadc38bc1bd9fa70fcfb4e23e8d5 Wed Mar 18 08:06:52 2020 -0700
    adding details about 119 and 44 way conservation tracks, refs #25090
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    92565d0dde74969729cf021838a55e94fe3147ba Wed Mar 18 09:10:10 2020 -0700
    adding the 44-way with strain names refs #25090
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    024fff8aa011bb0300e20776ad95e486c5eeec62 Thu Mar 19 08:45:54 2020 -0700
    Fixing up uniprot track trackDbs for wuhCor1,refs #25192
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    262feb6d94b84b2d407cf1454dc1e49b6e865da9 Fri Mar 20 12:07:25 2020 -0700
    new NCBI genes on dev only for the moment
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    fd95861dbf3dd970c833b11076daa0da8738b1e8 Fri Mar 20 16:43:31 2020 -0700
    Adding 3 tracks derived from nextstrain.org: Nextstrain {Genes, Clades, Variants}. refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.strainName44way.ra
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    92565d0dde74969729cf021838a55e94fe3147ba Wed Mar 18 09:10:10 2020 -0700
    adding the 44-way with strain names refs #25090
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    449553d2b9dbbe845fb8c5fc2fca9bf016297650 Wed Mar 18 09:14:35 2020 -0700
    using html for cons44way refs #25090
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    b8d4a65b4dd1c477971a7d8f6c97ef8a6bc71e2d Wed Mar 18 09:21:51 2020 -0700
    updated short and long labels from Max update refs #25090
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    879041dca6623320be63dbcbfceaf82dec2bd49a Wed Mar 18 09:24:41 2020 -0700
    update default visibility refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
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    024fff8aa011bb0300e20776ad95e486c5eeec62 Thu Mar 19 08:45:54 2020 -0700
    Fixing up uniprot track trackDbs for wuhCor1,refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2AliSwissprot.html
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    024fff8aa011bb0300e20776ad95e486c5eeec62 Thu Mar 19 08:45:54 2020 -0700
    Fixing up uniprot track trackDbs for wuhCor1,refs #25192
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    dc70e2d06a40b4a4f32cb844f68b7f6a8ffe0a8e Sat Mar 21 12:56:17 2020 -0700
    Adding some line breaks to desc pages refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Interest.html
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    024fff8aa011bb0300e20776ad95e486c5eeec62 Thu Mar 19 08:45:54 2020 -0700
    Fixing up uniprot track trackDbs for wuhCor1,refs #25192
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    dc70e2d06a40b4a4f32cb844f68b7f6a8ffe0a8e Sat Mar 21 12:56:17 2020 -0700
    Adding some line breaks to desc pages refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/uniprotCov2.html
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    024fff8aa011bb0300e20776ad95e486c5eeec62 Thu Mar 19 08:45:54 2020 -0700
    Fixing up uniprot track trackDbs for wuhCor1,refs #25192
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    dc70e2d06a40b4a4f32cb844f68b7f6a8ffe0a8e Sat Mar 21 12:56:17 2020 -0700
    Adding some line breaks to desc pages refs #25192
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
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    e54336367a81683a7004b762b64e064a8ee9ded3 Thu Mar 19 08:55:03 2020 -0700
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/near/hgNear/association.c
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    b63c6cd3032d2395c889cb0a58b28464d9d7f6a6 Tue Mar 17 09:01:34 2020 -0700
    fix some of the problems from #25160
• src/hg/utils/automation/doNcbiRefSeq.pl
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    7f4217b12c9e6a7185a37ebc4d43c40cab29b85c Fri Mar 20 13:41:16 2020 -0700
    errro out when all files can not be found refs #24547
• src/hg/utils/automation/perlPara.pl
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    84de43168bbf2952470fb8757c79a585c8668a8a Fri Mar 20 14:28:31 2020 -0700
    useful script to run a list of commands in a fashion similar to a parasol batch refs #24547
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    fd95861dbf3dd970c833b11076daa0da8738b1e8 Fri Mar 20 16:43:31 2020 -0700
    Adding 3 tracks derived from nextstrain.org: Nextstrain {Genes, Clades, Variants}. refs #25188
• src/hg/utils/otto/nextstrainNcov/makefile
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    fd95861dbf3dd970c833b11076daa0da8738b1e8 Fri Mar 20 16:43:31 2020 -0700
    Adding 3 tracks derived from nextstrain.org: Nextstrain {Genes, Clades, Variants}. refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    fd95861dbf3dd970c833b11076daa0da8738b1e8 Fri Mar 20 16:43:31 2020 -0700
    Adding 3 tracks derived from nextstrain.org: Nextstrain {Genes, Clades, Variants}. refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrainClade.as
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    fd95861dbf3dd970c833b11076daa0da8738b1e8 Fri Mar 20 16:43:31 2020 -0700
    Adding 3 tracks derived from nextstrain.org: Nextstrain {Genes, Clades, Variants}. refs #25188
• src/inc/vcf.h
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    5c8f8925eb335bb375595e839368c3f7594ea7e4 Mon Mar 16 12:24:10 2020 -0700
    Libify code that counts genotypes correctly from vcfClick.c and use it in vcfTrack.c. refs #24623, fixes #25165
• src/lib/vcf.c
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    5c8f8925eb335bb375595e839368c3f7594ea7e4 Mon Mar 16 12:24:10 2020 -0700
    Libify code that counts genotypes correctly from vcfClick.c and use it in vcfTrack.c. refs #24623, fixes #25165
• src/utils/qa/weeklybld/buildEnv.csh
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    eed2460f436569aacf67430cb39bac6283daac60 Mon Mar 23 10:01:10 2020 -0700
    v396 preview2, refs #25191

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