All File Changes

v401_preview2 to v401_base (2020-07-06 to 2020-07-13) v401

• confs/asia.hg.conf
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    1bc43494c9580d4f5f065fb5d890854b3a0fdb79 Sun Jul 12 01:11:41 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    1bc43494c9580d4f5f065fb5d890854b3a0fdb79 Sun Jul 12 01:11:41 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
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    1bc43494c9580d4f5f065fb5d890854b3a0fdb79 Sun Jul 12 01:11:41 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/gencodeSection.c
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    7ec945c514178edf4a609753dd28102f98e2f786 Sat Jul 11 10:02:25 2020 -0700
    some fixes in response to code review
• src/hg/hgGene/hgGene.h
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    7ec945c514178edf4a609753dd28102f98e2f786 Sat Jul 11 10:02:25 2020 -0700
    some fixes in response to code review
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, context: html, text, full: html, text
    791097ea7589f6fadcf825c5c3a8934054917a28 Thu Jul 9 14:38:12 2020 -0700
    VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC). refs #25870
• src/hg/hgTracks/variation.c
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    791097ea7589f6fadcf825c5c3a8934054917a28 Thu Jul 9 14:38:12 2020 -0700
    VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC). refs #25870
• src/hg/hgTracks/vcfTrack.c
  • lines changed 494, context: html, text, full: html, text
    791097ea7589f6fadcf825c5c3a8934054917a28 Thu Jul 9 14:38:12 2020 -0700
    VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC). refs #25870
• src/hg/htdocs/FAQ/FAQgenes.html
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    9a1f501b29a065739622c6c74e62e7d37a9dc4ba Thu Jul 9 06:15:32 2020 -0700
    extending genes faq with mito description, refs #25845
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    cb5adc121fe56896ad3167b96f150ce3a5fa973c Thu Jul 9 12:11:31 2020 -0700
    Slight modifications to Max's new mitochondria FAQ #25845
• src/hg/htdocs/FAQ/FAQreleases.html
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    0e243069902c33d6261956f52466f6bd95f09fe0 Thu Jul 9 10:34:52 2020 -0700
    Adding new assembly canFam4 to FAQreleases #25279
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    58d4abbed70bdae77be9fd3c4cb3c0e64526dc2a Thu Jul 9 11:13:37 2020 -0700
    Adding new assembly panPan3 to FAQreleases #25720
• src/hg/htdocs/goldenPath/credits.html
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    3af541b81411fb2ff75ac3275c97f0ec31326cc9 Thu Jul 9 10:40:53 2020 -0700
    Adding new assembly canFam4 to credits.html #25279
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    4283d8d7337b295f5f02f6c8a3a0a70eb3bb472b Thu Jul 9 11:15:43 2020 -0700
    Adding new assembly panPan3 to credits.html #25720
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    dc61362883ce0359695d92ecf6b84364a7a12457 Sun Jul 12 17:43:31 2020 -0700
    update bonobo credits
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 16, context: html, text, full: html, text
    1a02f1ea718003c05a9e29bd233029a81fc68bc5 Thu Jul 9 15:45:26 2020 -0700
    Clarifying baseColorDefault #25868
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
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    1a02f1ea718003c05a9e29bd233029a81fc68bc5 Thu Jul 9 15:45:26 2020 -0700
    Clarifying baseColorDefault #25868
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 44, context: html, text, full: html, text
    b85eedd6e445410736ede598ad401c6c68bee48d Tue Jul 7 15:16:50 2020 -0700
    Announcing covid tracks and 20th anniversary refs #25644
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    de2a75ea99144d175a1708df37b7569dd6cc23ac Tue Jul 7 15:46:02 2020 -0700
    Fixing type refs #25644
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    ff9a1f52471a92e4e00a987d372b6d7165e5552e Wed Jul 8 17:23:07 2020 -0700
    fixing date on announcement
  • lines changed 67, context: html, text, full: html, text
    45aff60448645331b37278bb57faa67a2e0a7825 Thu Jul 9 14:03:01 2020 -0700
    Adding new assembly panPan3 to newsArch page #25720
• src/hg/htdocs/indexNews.html
  • lines changed 16, context: html, text, full: html, text
    b85eedd6e445410736ede598ad401c6c68bee48d Tue Jul 7 15:16:50 2020 -0700
    Announcing covid tracks and 20th anniversary refs #25644
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    ff9a1f52471a92e4e00a987d372b6d7165e5552e Wed Jul 8 17:23:07 2020 -0700
    fixing date on announcement
  • lines changed 12, context: html, text, full: html, text
    dcab2c7a07fbc397c198b2d402698cd3822d1dd6 Thu Jul 9 14:06:17 2020 -0700
    Adding new assembly panPan3 to indexNews page #25720
• src/hg/inc/vcfUi.h
  • lines changed 1, context: html, text, full: html, text
    791097ea7589f6fadcf825c5c3a8934054917a28 Thu Jul 9 14:38:12 2020 -0700
    VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC). refs #25870
• src/hg/inc/versionInfo.h
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    40cd595d31dd07aedc461b8792a9a9297348570b Mon Jul 13 09:59:24 2020 -0700
    New version number v401
• src/hg/lib/vcfUi.c
  • lines changed 11, context: html, text, full: html, text
    791097ea7589f6fadcf825c5c3a8934054917a28 Thu Jul 9 14:38:12 2020 -0700
    VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC). refs #25870
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    20516ed66388b4f70b37e243746c3edeb82e2123 Mon Jul 6 11:35:22 2020 -0700
    Turning on GenBank updates for new assembly #25720
• src/hg/makeDb/outside/gencode/lib/gencode/biotypes.py
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    f414f1cc77160930c8874076c32379141e92f0c2 Mon Jul 6 11:15:08 2020 -0700
    fix build in computing gencode transcript class for some pseudogenes
• src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.attrs
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    f414f1cc77160930c8874076c32379141e92f0c2 Mon Jul 6 11:15:08 2020 -0700
    fix build in computing gencode transcript class for some pseudogenes
• src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tags
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    f414f1cc77160930c8874076c32379141e92f0c2 Mon Jul 6 11:15:08 2020 -0700
    fix build in computing gencode transcript class for some pseudogenes
• src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tsl
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    f414f1cc77160930c8874076c32379141e92f0c2 Mon Jul 6 11:15:08 2020 -0700
    fix build in computing gencode transcript class for some pseudogenes
• src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tsv
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    f414f1cc77160930c8874076c32379141e92f0c2 Mon Jul 6 11:15:08 2020 -0700
    fix build in computing gencode transcript class for some pseudogenes
• src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.attrs
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.tsv
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.attrs
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.tsv
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.attrs
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.tsv
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.attrs
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.tsv
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.attrs
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.tsv
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.attrs
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.tsv
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.attrs
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.tsv
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    110f9f8aa88ddabda2d95303f68c8f0a54274129 Mon Jul 6 12:37:58 2020 -0700
    updated some test results for pseudo change
• src/hg/makeDb/outside/gencode/tests/input/pseudo.gff3
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    f414f1cc77160930c8874076c32379141e92f0c2 Mon Jul 6 11:15:08 2020 -0700
    fix build in computing gencode transcript class for some pseudogenes
• src/hg/makeDb/outside/gencode/tests/makefile
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    f414f1cc77160930c8874076c32379141e92f0c2 Mon Jul 6 11:15:08 2020 -0700
    fix build in computing gencode transcript class for some pseudogenes
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    791097ea7589f6fadcf825c5c3a8934054917a28 Thu Jul 9 14:38:12 2020 -0700
    VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC). refs #25870
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
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    8744bfce66c49ab3e327314a7aaa2d8b8ee0e58c Wed Jul 8 17:13:19 2020 -0700
    adding link to APPRIS paper
• src/hg/makeDb/trackDb/human/hg38/trackDb.mito204way.ra
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    fe1baab542a09943209bf803a3082a339bba8126 Wed Jul 8 11:37:13 2020 -0700
    adding 204-way vertebrate mitochondria multiple alignment refs #11636
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    bfb513b65a6e5f6a510c307f213d1365f6227c65 Wed Jul 8 12:19:57 2020 -0700
    add TBA 204-way track refs #11636
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    fe1baab542a09943209bf803a3082a339bba8126 Wed Jul 8 11:37:13 2020 -0700
    adding 204-way vertebrate mitochondria multiple alignment refs #11636
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    791097ea7589f6fadcf825c5c3a8934054917a28 Thu Jul 9 14:38:12 2020 -0700
    VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC). refs #25870
• src/hg/makeDb/trackDb/tagTypes.tab
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    791097ea7589f6fadcf825c5c3a8934054917a28 Thu Jul 9 14:38:12 2020 -0700
    VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC). refs #25870
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainFreq.html
  • lines changed 11, context: html, text, full: html, text
    77281e609914980bd726570382a83700597651ba Fri Jul 10 12:31:23 2020 -0700
    Adding double quotes around HTML attributes, reefs #25481
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    8ff979385af2c750fe219a12ca78be5941878df9 Mon Jul 13 03:36:12 2020 -0700
    Adding command-line extraction examples and replacing double quotes with HTML entities, refs #25481
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    0adc01955a6ca5108d97852837af83fc9cd221a7 Mon Jul 13 03:41:41 2020 -0700
    Adding information about the Data Access FAQ, refs #25481
• src/hg/makeDb/trackDb/virus/wuhCor1/phylocsf.ra
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    fc3c899668b75574307cb47d7182d812afbf3d05 Tue Jul 7 16:45:24 2020 -0700
    Adding/ fixing pennant icons for wuhCor1 refs #25644
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.7way.ra
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    fc3c899668b75574307cb47d7182d812afbf3d05 Tue Jul 7 16:45:24 2020 -0700
    Adding/ fixing pennant icons for wuhCor1 refs #25644
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
  • lines changed 2, context: html, text, full: html, text
    791097ea7589f6fadcf825c5c3a8934054917a28 Thu Jul 9 14:38:12 2020 -0700
    VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC). refs #25870
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    fc3c899668b75574307cb47d7182d812afbf3d05 Tue Jul 7 16:45:24 2020 -0700
    Adding/ fixing pennant icons for wuhCor1 refs #25644
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
  • lines changed 15, context: html, text, full: html, text
    9e80f014450e66198b33e2c46cd6bc51baec3c9a Fri Jul 10 02:51:04 2020 -0700
    converting uniprot track to bigGenePred, email from Jim, no redmine yet
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 1, context: html, text, full: html, text
    7bfc388f05fccd163c067d3a7f2bf7a738b00e03 Mon Jul 13 09:26:44 2020 -0700
    correctly adding md5sum of net.gz to the md5sum.txt file refs #25279
• src/inc/srcVersion.h
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    40cd595d31dd07aedc461b8792a9a9297348570b Mon Jul 13 09:59:24 2020 -0700
    New version number v401
• src/lib/phyloTree.c
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    fdd15dd4ea30b1f9f319ff22bc2858f00c7aa8ed Fri Jul 10 13:49:45 2020 -0700
    strtod is faster than sscanf; when parsing a tree with ~61k node lengths, it makes a difference of >3s.
• src/utils/qa/weeklybld/buildEnv.csh
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    1052a1ef23c2788f2dc7badf7aa758f1626fd510 Mon Jul 13 09:53:45 2020 -0700
    v401 final build

• lines changed: 1040
• files changed: 68