All File Changes

v402_base to v403_preview (2020-08-03 to 2020-08-10) v403

• src/hg/hgTracks/menu.c
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    65fcb3ab152cbdb58c38426e0736efd158a1d711 Wed Aug 5 15:33:50 2020 -0700
    Fix problem with right-click when recTrackSets .tab file is present, but menu doesn't have hook (protect GBIB ?). refs #25601
• src/hg/hgTracks/vcfTrack.c
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    6a8d7741dd91b8c219f367c285f5800bd389ea9b Mon Aug 10 06:02:48 2020 -0700
    Remove some debug code, #25996
• src/hg/htdocs/covid19.html
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    1eafcf08a92af13301da1e1781779a19914f49f5 Tue Aug 4 06:23:01 2020 -0700
    adding GISAID links to wuhCor1 desc pages, refs #26008
• src/hg/htdocs/goldenPath/help/bigBed.html
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    76cf2d3e885d0a9f1473c703908d89f745f8fb9d Fri Aug 7 10:34:22 2020 -0700
    Adding another sentence to step 6 of the bigBed doc to help with what hosting means, refs #26004
• src/hg/htdocs/goldenPath/newsarch.html
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    74e2da5dec6a273fb4c2507ba8b70312451222da Mon Aug 3 10:22:48 2020 -0700
    Announcing rheMac10 annotated SNVs track refs #25602
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    290fb8b209f3e757bd963d600bf575a6c9d3c78c Mon Aug 3 12:37:42 2020 -0700
    fixed ugly typo
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    791fedf2a50003798bff046bd22f01bb16af3ea0 Thu Aug 6 17:56:23 2020 -0700
    Draft annoucement for Covid track release refs #25984
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    098ce410adc713ba343ee53ea8325a2d62ad0710 Thu Aug 6 18:03:52 2020 -0700
    typo fix #25984
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    58abbfd0de1d594241efa28e54f3886f28e3433a Fri Aug 7 10:46:35 2020 -0700
    Fixing grammar typos #25984
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    22761c54344596682ec83093ec29c6acfabffbf5 Fri Aug 7 10:49:25 2020 -0700
    Fixing grammar typos #25984
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    a1b107fdb30e455d3928a235e3f5d18cbc4f0d25 Fri Aug 7 11:07:04 2020 -0700
    Adding info refs #25984
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    74e2da5dec6a273fb4c2507ba8b70312451222da Mon Aug 3 10:22:48 2020 -0700
    Announcing rheMac10 annotated SNVs track refs #25602
  • lines changed 13, context: html, text, full: html, text
    791fedf2a50003798bff046bd22f01bb16af3ea0 Thu Aug 6 17:56:23 2020 -0700
    Draft annoucement for Covid track release refs #25984
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    d857333f37b521d46ab975a4eed01865b13606a8 Fri Aug 7 10:57:59 2020 -0700
    Cuttiung chars #25984
• src/hg/lib/hdb.c
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    ae7c5702e2f43ed446fe678fefbb9f30e26db9f3 Mon Aug 3 12:49:13 2020 -0700
    Added missing call to cloneString in hdbDefaultKnownDb. refs #26002
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    dae62f0954272b7d989ca5c6195b3069dd2eaa93 Mon Aug 3 13:04:45 2020 -0700
    Use string comparison instead of pointer equality (cart db is not a constant; symptoms if position search is unsuccessful). refs #26002
• src/hg/lib/vcfUi.c
  • lines changed 6, context: html, text, full: html, text
    8f064cfff5b905949513f7b410f1bcd85d52100b Tue Aug 4 12:22:33 2020 -0700
    Add info icon and text for trio de novo color, refs #25983
• src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py
  • lines changed 215, context: html, text, full: html, text
    3bd75282155497633f910125db685ee498944b17 Thu Aug 6 11:48:44 2020 -0700
    Big update to the script. Added options to output indivisual stats or all at once. Script now only works on Chris Lee's combined and filtered log format. Script also outputs messages about it's progress through outputting files and tells you the output directory. no redmine
• src/hg/makeDb/doc/hg19.txt
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    90722fe965a89529d622dc70225dea8cf3924e32 Tue Aug 4 16:53:00 2020 -0700
    Stage genome in a bottle trio vcf track, refs #25873
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    73beb2ce1a8cef6d6e33fb28f95d5871c89d47f1 Wed Aug 5 15:50:31 2020 -0700
    starting work on clinsub track
• src/hg/makeDb/doc/hg38/variation.txt
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    90722fe965a89529d622dc70225dea8cf3924e32 Tue Aug 4 16:53:00 2020 -0700
    Stage genome in a bottle trio vcf track, refs #25873
• src/hg/makeDb/giab/download.sh
  • lines changed 47, context: html, text, full: html, text
    90722fe965a89529d622dc70225dea8cf3924e32 Tue Aug 4 16:53:00 2020 -0700
    Stage genome in a bottle trio vcf track, refs #25873
• src/hg/makeDb/giab/make.txt
  • lines changed 16, context: html, text, full: html, text
    90722fe965a89529d622dc70225dea8cf3924e32 Tue Aug 4 16:53:00 2020 -0700
    Stage genome in a bottle trio vcf track, refs #25873
• src/hg/makeDb/giab/mergeVcfs.sh
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    90722fe965a89529d622dc70225dea8cf3924e32 Tue Aug 4 16:53:00 2020 -0700
    Stage genome in a bottle trio vcf track, refs #25873
• src/hg/makeDb/trackDb/human/clinGen.html
  • lines changed 54, context: html, text, full: html, text
    71e02fc571b87f50f6d984f0cbc4954595f651c1 Mon Aug 3 17:08:52 2020 -0700
    finished description page ClinGen composite ref #24818
• src/hg/makeDb/trackDb/human/hg19/clinsub.ra
  • lines changed 6, context: html, text, full: html, text
    73beb2ce1a8cef6d6e33fb28f95d5871c89d47f1 Wed Aug 5 15:50:31 2020 -0700
    starting work on clinsub track
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    73beb2ce1a8cef6d6e33fb28f95d5871c89d47f1 Wed Aug 5 15:50:31 2020 -0700
    starting work on clinsub track
• src/hg/makeDb/trackDb/human/hg38/omimGene2.html
  • lines changed 8, context: html, text, full: html, text
    bcfd0204545186c59bf40fa9472014aab0cf16f6 Fri Jul 31 16:45:19 2020 -0700
    Slight modifications for omim Data Access #18419
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    c94a801cfbb5199f1e77b215d3c7bf15d0420faa Thu Aug 6 16:03:43 2020 -0700
    Local links and type fix for CR refs #25995
• src/hg/makeDb/trackDb/human/hg38/tgpTrios.html
  • lines changed 29, context: html, text, full: html, text
    757048a1b97a53312b7636dcf458efaf76599d90 Tue Aug 4 12:15:07 2020 -0700
    Fixing up 1000 Genomes trio track description to describe new color options, refs #25983
• src/hg/makeDb/trackDb/human/omimGene2.html
  • lines changed 8, context: html, text, full: html, text
    bcfd0204545186c59bf40fa9472014aab0cf16f6 Fri Jul 31 16:45:19 2020 -0700
    Slight modifications for omim Data Access #18419
  • lines changed 2, context: html, text, full: html, text
    c94a801cfbb5199f1e77b215d3c7bf15d0420faa Thu Aug 6 16:03:43 2020 -0700
    Local links and type fix for CR refs #25995
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 3, context: html, text, full: html, text
    9862c23b1fd02807f3a005eec30ec76412884726 Mon Aug 3 17:14:37 2020 -0700
    standarized track names, shortened short label refs #24818
  • lines changed 5, context: html, text, full: html, text
    6bccfc2f21760e12c7203e99694f02b4499b9354 Tue Aug 4 09:46:03 2020 -0700
    Override default alphabetic on shortLabel ordering of clinGen composite tracks and get URLs to pubmed working, refs #24818
• src/hg/makeDb/trackDb/human/trackDb.giab.ra
  • lines changed 45, context: html, text, full: html, text
    90722fe965a89529d622dc70225dea8cf3924e32 Tue Aug 4 16:53:00 2020 -0700
    Stage genome in a bottle trio vcf track, refs #25873
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    7d169d1245946d2eb9cf2d6f65adf2fc56ef0b35 Wed Aug 5 14:06:59 2020 -0700
    Stage genome in a bottle structural variants on dev, refs #24349
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 37, context: html, text, full: html, text
    5f856345200f8861b168c85d45e267010d6b55e4 Mon Aug 3 16:40:33 2020 -0700
    Update LOVD to bigBed, refs #25841
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    90722fe965a89529d622dc70225dea8cf3924e32 Tue Aug 4 16:53:00 2020 -0700
    Stage genome in a bottle trio vcf track, refs #25873
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
  • lines changed 2, context: html, text, full: html, text
    1eafcf08a92af13301da1e1781779a19914f49f5 Tue Aug 4 06:23:01 2020 -0700
    adding GISAID links to wuhCor1 desc pages, refs #26008
• src/hg/makeDb/trackDb/virus/wuhCor1/phyloGenes.html
  • lines changed 13, context: html, text, full: html, text
    da1ce55c24092888b3a58178290620e98fcbdf2a Thu Jul 30 19:17:22 2020 -0400
    Changes to phyloGenes.html, including renaming ORF3b-2 -> ORF3d
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    ed66dc448213f70406781a0a3ab6a2f27f6b26bb Fri Jul 31 14:40:52 2020 -0400
    Used shorter ORF3b in phyloGenes.html
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
  • lines changed 5, context: html, text, full: html, text
    790b76f55018799ced7abdbbda37a152bb420c73 Mon Aug 3 14:45:06 2020 -0700
    Cluster-admin have enabled otto-push of Nextstrain tracks; update & add pennant icons to reflect that.
• src/hg/near/hgNear/hgNearData/Human/hg38/genome.ra
  • lines changed 1, context: html, text, full: html, text
    1c1d12325f1ee9cf1d2bb092dbc6d6c4fa878e26 Mon Aug 3 15:11:44 2020 -0700
    remove externalDb because we haven't pushed the database
• src/hg/utils/otto/clinGen/processClinGenDosage.py
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    c8cf0851df29747fc97ace2912d452ac4d815b45 Mon Aug 10 06:24:35 2020 -0700
    Fixing some problems in clinGenDosage otto job after code review feedback, refs #25996
• src/hg/utils/otto/dbVar/checkDbVar.sh
  • lines changed 5, context: html, text, full: html, text
    7d169d1245946d2eb9cf2d6f65adf2fc56ef0b35 Wed Aug 5 14:06:59 2020 -0700
    Stage genome in a bottle structural variants on dev, refs #24349
• src/hg/utils/otto/dbVar/checkNstd175.sh
  • lines changed 80, context: html, text, full: html, text
    7d169d1245946d2eb9cf2d6f65adf2fc56ef0b35 Wed Aug 5 14:06:59 2020 -0700
    Stage genome in a bottle structural variants on dev, refs #24349
• src/hg/utils/otto/dbVar/giabSv.as
  • lines changed 23, context: html, text, full: html, text
    7d169d1245946d2eb9cf2d6f65adf2fc56ef0b35 Wed Aug 5 14:06:59 2020 -0700
    Stage genome in a bottle structural variants on dev, refs #24349
• src/hg/utils/otto/dbVar/makefile
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    7d169d1245946d2eb9cf2d6f65adf2fc56ef0b35 Wed Aug 5 14:06:59 2020 -0700
    Stage genome in a bottle structural variants on dev, refs #24349
• src/hg/utils/otto/dbVar/processNstd175.py
  • lines changed 149, context: html, text, full: html, text
    7d169d1245946d2eb9cf2d6f65adf2fc56ef0b35 Wed Aug 5 14:06:59 2020 -0700
    Stage genome in a bottle structural variants on dev, refs #24349
• src/hg/utils/otto/lovd/checkAndLoad.sh
  • lines changed 15, context: html, text, full: html, text
    5f856345200f8861b168c85d45e267010d6b55e4 Mon Aug 3 16:40:33 2020 -0700
    Update LOVD to bigBed, refs #25841
• src/hg/utils/otto/lovd/download.sh
  • lines changed 4, context: html, text, full: html, text
    5f856345200f8861b168c85d45e267010d6b55e4 Mon Aug 3 16:40:33 2020 -0700
    Update LOVD to bigBed, refs #25841
• src/hg/utils/otto/lovd/lovd.as
  • lines changed 12, context: html, text, full: html, text
    5f856345200f8861b168c85d45e267010d6b55e4 Mon Aug 3 16:40:33 2020 -0700
    Update LOVD to bigBed, refs #25841
• src/hg/utils/otto/lovd/makefile
  • lines changed 1, context: html, text, full: html, text
    5f856345200f8861b168c85d45e267010d6b55e4 Mon Aug 3 16:40:33 2020 -0700
    Update LOVD to bigBed, refs #25841
• src/hg/visiGene/vgGetText/vgGetText.c
  • lines changed 3, context: html, text, full: html, text
    d576a4c24545bb01c2ad375f733f4c82d98ab268 Mon Aug 3 12:17:04 2020 -0700
    fix up dependency on kgXref
• src/lib/fof.c
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    cb491cef9bf0ed30c70a6223e134aba708e0afa1 Thu Jul 23 06:37:12 2020 -0500
    Use fileno() to obtain integer file descriptor from FILE * Fixes musl "error: arithmetic on pointer to an incomplete type"
• src/lib/udc.c
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    ef11ad850abf574a711938786d3f0cc04f6f7127 Fri Jul 24 05:28:31 2020 -0500
    Use POSIX pathconf() instead of BSD MAXNAMLEN
• src/utils/qa/weeklybld/buildEnv.csh
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    0f2f65b43a290f74508e9ccc05973702a64905a4 Mon Aug 10 10:05:24 2020 -0700
    v403 preview1

• lines changed: 981
• files changed: 57