All File Changes

v419_preview2 to v419_base (2021-08-09 to 2021-08-16) v419

• src/hg/hgTracks/wigMafTrack.c
  • lines changed 17, context: html, text, full: html, text
    c41061d1a7eed8c0882224a8b1ea898fd356fa20 Fri Aug 13 11:26:22 2021 -0700
    fix bigMaf frames code to pay attention to the species... d'oho
• src/hg/hgc/clinvarSubLolly.c
  • lines changed 1, context: html, text, full: html, text
    f9d16c71532bbc7a8e1e873d194ae1c937315686 Thu Aug 12 12:50:58 2021 -0700
    print out HTML and schema for Clinvar Submissions track
• src/hg/htdocs/goldenPath/help/hubQuickStartFilter.html
  • lines changed 1, context: html, text, full: html, text
    80d589084d4b169e4caf54c80472377061ce8c24 Tue Aug 10 16:44:49 2021 -0700
    Adding a missing .as file to filter page, refs #27976
• src/hg/inc/cart.h
  • lines changed 5, context: html, text, full: html, text
    46cacb52f48b67dbdbb131af561827f3f5357a20 Tue Aug 10 13:20:23 2021 -0700
    add utility to make a cartEdit that supports movinb existing tracks to a superTrack . Add a new cartEdit1 to move a bunch of tracks to three new supertracks
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    945ea737087057c1190caded309a53537333ea0b Mon Aug 16 10:11:46 2021 -0700
    New version number v419
• src/hg/lib/cartEdit0.c
  • lines changed 120, context: html, text, full: html, text
    46cacb52f48b67dbdbb131af561827f3f5357a20 Tue Aug 10 13:20:23 2021 -0700
    add utility to make a cartEdit that supports movinb existing tracks to a superTrack . Add a new cartEdit1 to move a bunch of tracks to three new supertracks
• src/hg/lib/cartEdit1.c
  • lines changed 39, context: html, text, full: html, text
    46cacb52f48b67dbdbb131af561827f3f5357a20 Tue Aug 10 13:20:23 2021 -0700
    add utility to make a cartEdit that supports movinb existing tracks to a superTrack . Add a new cartEdit1 to move a bunch of tracks to three new supertracks
• src/hg/lib/cartRewrite.c
  • lines changed 171, context: html, text, full: html, text
    46cacb52f48b67dbdbb131af561827f3f5357a20 Tue Aug 10 13:20:23 2021 -0700
    add utility to make a cartEdit that supports movinb existing tracks to a superTrack . Add a new cartEdit1 to move a bunch of tracks to three new supertracks
• src/hg/lib/hgFind.c
  • lines changed 13, context: html, text, full: html, text
    a73cea4b50ac605516110de8e7db5b25b1f0e793 Tue Aug 10 10:19:26 2021 -0700
    Fix bug I recently introduced when searching for old accessions in hgvs search, refs #27942
• src/hg/lib/hgMaf.c
  • lines changed 4, context: html, text, full: html, text
    13e8fdadc6ab46c89eed7516344d3fda54b6c998 Fri Aug 13 14:56:38 2021 -0700
    get the maf blocks in the right order so the draw engine doesn't get confused. Also a little speed-up
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    46cacb52f48b67dbdbb131af561827f3f5357a20 Tue Aug 10 13:20:23 2021 -0700
    add utility to make a cartEdit that supports movinb existing tracks to a superTrack . Add a new cartEdit1 to move a bunch of tracks to three new supertracks
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    8deb467d374bb1670ab6dcf127d566191df56ef8 Mon Aug 9 10:29:31 2021 -0700
    update with 34 fungi, 10 mammals, 10 fish, 9 invertebrates, 6 birds, 4 vertebrate, 4 plants refs #23891
  • lines changed 77, context: html, text, full: html, text
    98365ec2d3f48f0df6ec73cbf95aee1c538171a9 Mon Aug 9 10:32:03 2021 -0700
    update with 34 fungi, 10 mammals, 10 fish, 9 invertebrates, 6 birds, 4 vertebrate, 4 plants refs #23891
  • lines changed 8, context: html, text, full: html, text
    9dc979a8ee168053a113e76c8588ecdcb13a2730 Tue Aug 10 13:47:31 2021 -0700
    adding 1 bird, fish, fungi, vertebrate, and 2 invertebrates, plants refs #23891
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    091bcab3da87d766f547a29353cce5b6d2791204 Tue Aug 10 17:58:39 2021 -0700
    add 3 plants refs #23891
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 13, context: html, text, full: html, text
    9dd66185c2c7514131595f31615ac9afe2a6393f Wed Aug 11 16:10:17 2021 -0700
    adding 7 new assemblies refs #23891
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    10fbc9ddee0b5e0ba7740bdad9ac7f6e95502dc7 Wed Aug 11 15:06:16 2021 -0700
    adding 12 new assemblies refs #23891
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 469, context: html, text, full: html, text
    5dc9c100d8653cf25b6fdc26d4565e5f440c29dc Wed Aug 11 14:17:09 2021 -0700
    update with 35 new assemblies refs #27072
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 18, context: html, text, full: html, text
    29a00b93a02141b7835d2ab660723cff4a03b05a Thu Aug 12 11:16:13 2021 -0700
    adding 11 new assemblies refs #23891
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    90e55e6a1ce5183ab418ffe94f27bd5dcd7897ee Thu Aug 12 12:25:33 2021 -0700
    ten assemblies have aged out refs #23891
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    dfc875cf50fb8f376023cf7ea9c224b71d8dd9bd Wed Aug 11 11:21:30 2021 -0700
    adding 10 new genomes refs #23891
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 37, context: html, text, full: html, text
    0177691f58a34bb75df032f96cce0899c1bddbe5 Thu Aug 12 12:04:07 2021 -0700
    catch up nine new assemblies refs #23891
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    c76a73ca8e50787bcec73c80a63618eca166edf0 Wed Aug 11 15:43:36 2021 -0700
    adding 5 new assemblies refs #23891
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 7, context: html, text, full: html, text
    95ac7607e394e7daab5bec99238e7db860b4849b Fri Aug 13 17:09:31 2021 -0700
    Updating clinvar filters and clarifying the clinvar interp desc page to explain bead sizes, refs #27991
• src/hg/makeDb/trackDb/human/hg19/affyArchive.ra
  • lines changed 1, context: html, text, full: html, text
    0d805b77ae6253aec6316dfda0ffd9bf857771b7 Wed Aug 11 10:48:32 2021 -0700
    add cartVersion 2 to the new archive super tracks
• src/hg/makeDb/trackDb/human/hg19/genePredArchive.ra
  • lines changed 1, context: html, text, full: html, text
    0d805b77ae6253aec6316dfda0ffd9bf857771b7 Wed Aug 11 10:48:32 2021 -0700
    add cartVersion 2 to the new archive super tracks
• src/hg/makeDb/trackDb/human/hg19/tgpArchive.ra
  • lines changed 1, context: html, text, full: html, text
    0d805b77ae6253aec6316dfda0ffd9bf857771b7 Wed Aug 11 10:48:32 2021 -0700
    add cartVersion 2 to the new archive super tracks
• src/hg/makeDb/trackDb/human/hg38/affyArchive.ra
  • lines changed 1, context: html, text, full: html, text
    0d805b77ae6253aec6316dfda0ffd9bf857771b7 Wed Aug 11 10:48:32 2021 -0700
    add cartVersion 2 to the new archive super tracks
• src/hg/makeDb/trackDb/human/hg38/genePredArchive.ra
  • lines changed 1, context: html, text, full: html, text
    0d805b77ae6253aec6316dfda0ffd9bf857771b7 Wed Aug 11 10:48:32 2021 -0700
    add cartVersion 2 to the new archive super tracks
• src/hg/makeDb/trackDb/human/hg38/spliceAi.ra
  • lines changed 38, context: html, text, full: html, text
    7f64d7f557f0eb8d3d309aa6441db6cd1f108798 Thu Aug 12 15:13:58 2021 -0700
    simple ordinary VCF display of the SpliceAi VCF files refs #27141
• src/hg/makeDb/trackDb/human/hg38/tgpArchive.ra
  • lines changed 1, context: html, text, full: html, text
    0d805b77ae6253aec6316dfda0ffd9bf857771b7 Wed Aug 11 10:48:32 2021 -0700
    add cartVersion 2 to the new archive super tracks
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    7f64d7f557f0eb8d3d309aa6441db6cd1f108798 Thu Aug 12 15:13:58 2021 -0700
    simple ordinary VCF display of the SpliceAi VCF files refs #27141
• src/hg/makeDb/trackDb/human/revel.html
  • lines changed 2, context: html, text, full: html, text
    a5d3d4bd7884441ea780f8f3d6cef4e25452dd73 Fri Aug 13 11:42:35 2021 -0700
    small whitespace change
• src/hg/makeDb/trackDb/human/trackDb.clinvar.alpha.ra
  • lines changed 96, context: html, text, full: html, text
    95ac7607e394e7daab5bec99238e7db860b4849b Fri Aug 13 17:09:31 2021 -0700
    Updating clinvar filters and clarifying the clinvar interp desc page to explain bead sizes, refs #27991
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 8, context: html, text, full: html, text
    95ac7607e394e7daab5bec99238e7db860b4849b Fri Aug 13 17:09:31 2021 -0700
    Updating clinvar filters and clarifying the clinvar interp desc page to explain bead sizes, refs #27991
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    95ac7607e394e7daab5bec99238e7db860b4849b Fri Aug 13 17:09:31 2021 -0700
    Updating clinvar filters and clarifying the clinvar interp desc page to explain bead sizes, refs #27991
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    e29ca5ed760db9fd9e3c6be08241ba5d686a5f6a Fri Aug 13 15:42:13 2021 -0700
    Updating tracks priority for mm39, refs #27665
• src/hg/utils/automation/cleanGenePredOverSized.pl
  • lines changed 58, context: html, text, full: html, text
    db7ba618f0d684d8fd44e837ad3ce7e66d111bb9 Tue Aug 10 10:43:17 2021 -0700
    to help with difficulty of wrap-around genes on circular genomes refs #23891
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    dc84ca81ef20efb01d72785d65e9c6a73219e49d Tue Aug 10 10:46:36 2021 -0700
    to help with difficulty of wrap-around genes on circular genomes refs #23891
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    453c6b15ef9c37431ec50e004cc30d550c78c4a3 Tue Aug 10 11:15:51 2021 -0700
    command not needed, function is in genePredFilter
• src/hg/utils/cartEditSuperTrack/cartEditSuperTrack.c
  • lines changed 100, context: html, text, full: html, text
    46cacb52f48b67dbdbb131af561827f3f5357a20 Tue Aug 10 13:20:23 2021 -0700
    add utility to make a cartEdit that supports movinb existing tracks to a superTrack . Add a new cartEdit1 to move a bunch of tracks to three new supertracks
• src/hg/utils/cartEditSuperTrack/makefile
  • lines changed 3, context: html, text, full: html, text
    46cacb52f48b67dbdbb131af561827f3f5357a20 Tue Aug 10 13:20:23 2021 -0700
    add utility to make a cartEdit that supports movinb existing tracks to a superTrack . Add a new cartEdit1 to move a bunch of tracks to three new supertracks
• src/hg/utils/cartEditSuperTrack/tests/expected/cartEdit1.c
  • lines changed 39, context: html, text, full: html, text
    46cacb52f48b67dbdbb131af561827f3f5357a20 Tue Aug 10 13:20:23 2021 -0700
    add utility to make a cartEdit that supports movinb existing tracks to a superTrack . Add a new cartEdit1 to move a bunch of tracks to three new supertracks
• src/hg/utils/cartEditSuperTrack/tests/input/test1.txt
  • lines changed 18, context: html, text, full: html, text
    46cacb52f48b67dbdbb131af561827f3f5357a20 Tue Aug 10 13:20:23 2021 -0700
    add utility to make a cartEdit that supports movinb existing tracks to a superTrack . Add a new cartEdit1 to move a bunch of tracks to three new supertracks
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    945ea737087057c1190caded309a53537333ea0b Mon Aug 16 10:11:46 2021 -0700
    New version number v419
• src/utils/qa/checkSyncAndMetaDataAll.py
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    8248a457d0f538a99c0814b208878631c6487295 Mon Aug 9 12:15:37 2021 -0700
    Updating the cron for hgw2 to expect 3 table discrepancy due to the relatedTrack table in hg38, no RM
• src/utils/qa/weeklybld/buildEnv.csh
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    a55ae243c32671a304d76c1ec0b723f1da7398af Mon Aug 16 10:10:51 2021 -0700
    v419 final build, refs #27946

• lines changed: 1514
• files changed: 47