All File Changes

v403_base to v404_preview (2020-08-24 to 2020-08-31) v404

• confs/asia.hg.conf
  • lines changed 3, context: html, text, full: html, text
    9d489058b42696f4dbfac03aa1c1f55bf174fafe Sun Aug 30 01:11:45 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    9d489058b42696f4dbfac03aa1c1f55bf174fafe Sun Aug 30 01:11:45 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 5, context: html, text, full: html, text
    9d489058b42696f4dbfac03aa1c1f55bf174fafe Sun Aug 30 01:11:45 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    9d489058b42696f4dbfac03aa1c1f55bf174fafe Sun Aug 30 01:11:45 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/lolly.h
  • lines changed 2, context: html, text, full: html, text
    15e1169d1ba4e318b78a89bf0e09bbc1d033d950 Mon Aug 24 13:09:18 2020 -0700
    first cut at Franklin display #25405
• src/hg/hgTracks/lollyTrack.c
  • lines changed 79, context: html, text, full: html, text
    15e1169d1ba4e318b78a89bf0e09bbc1d033d950 Mon Aug 24 13:09:18 2020 -0700
    first cut at Franklin display #25405
  • lines changed 9, context: html, text, full: html, text
    aa82ced1f07ddc93917a4e70f269241283cbe84b Tue Aug 25 10:45:34 2020 -0700
    add mouseovers to clinsub
  • lines changed 1, context: html, text, full: html, text
    187cf63172a955321863f8ed87669e60cc678c01 Tue Aug 25 17:20:55 2020 -0700
    use name to click into hgc, not mouseOver
• src/hg/hgTracks/vcfTrack.c
  • lines changed 1, context: html, text, full: html, text
    29350302a2a43cdb727dbb38d760c2e0465b1228 Mon Aug 24 15:07:57 2020 -0700
    Tighten up the spacing for unphased trios after Jim feedback
  • lines changed 6, context: html, text, full: html, text
    f6133a3e4e9f571295e8e6c5b9ac9ea886b49826 Mon Aug 24 16:36:58 2020 -0700
    Fix vcf color by function when in intergenic region, refs #26108
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    3475b145fbe84f0bb11107d2a91683d055b4c71e Tue Aug 25 12:24:12 2020 -0700
    Don't try to add a related tracks section for assembly hubs, refs #26040
  • lines changed 2, context: html, text, full: html, text
    92da6e28140226da42c274fd8156c62697daf9c0 Wed Aug 26 11:24:36 2020 -0700
    bigLolly should get the number of fields from the bigBed rather than assuming it is 12
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/blatServers.gorGor6.hgcentral
  • lines changed 0, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/blatServers.gorGor6.hgcentralbeta
  • lines changed 2, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/blatServers.gorGor6.hgcentraltest
  • lines changed 2, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/covid19.html
  • lines changed 18, context: html, text, full: html, text
    4475cd6aa12bbf5ac823c29e01271e2f23b39d22 Tue Aug 25 13:13:22 2020 -0700
    Adding a list of datasets to cell browser section on covid page, refs #25773
• src/hg/htdocs/dbDb.gorGor6.hgcentral
  • lines changed 0, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/dbDb.gorGor6.hgcentralbeta
  • lines changed 1, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/dbDb.gorGor6.hgcentraltest
  • lines changed 1, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/defaultDb.gorGor6.hgcentral
  • lines changed 1, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/defaultDb.gorGor6.hgcentralbeta
  • lines changed 1, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/defaultDb.gorGor6.hgcentraltest
  • lines changed 1, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/genomeClade.gorGor6.hgcentral
  • lines changed 1, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/genomeClade.gorGor6.hgcentralbeta
  • lines changed 1, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/genomeClade.gorGor6.hgcentraltest
  • lines changed 1, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 16, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 8, context: html, text, full: html, text
    819fe0dd688e9a31a6e57e46f2bdc31d6c023150 Tue Aug 25 16:02:57 2020 -0700
    Minor edits for barChart squish refs #23679
  • lines changed 3, context: html, text, full: html, text
    ad31a8422ed162cd74ef85599fca749d0d076270 Tue Aug 25 16:16:41 2020 -0700
    Adding link to hgTracks on barChart.html #23679
  • lines changed 2, context: html, text, full: html, text
    c8eeddec8324662ee7f23caa047c29fb589dc68f Thu Aug 27 13:24:58 2020 -0700
    Code review 26101
  • lines changed 4, context: html, text, full: html, text
    67a404a4cd859fa5b44d69f0de454df659540d99 Thu Aug 27 14:56:06 2020 -0700
    Correcting tag for CR #26101
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    0dd49e5cd65cc9b5f17b049f57e04225a9ecd715 Fri Aug 28 14:01:53 2020 -0700
    small cosmetic changes
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 5, context: html, text, full: html, text
    80cee0de0c951f3db41a41e97fa6baa022d312a3 Fri Aug 28 13:09:56 2020 -0700
    Adding clarity on the spectrum options, no RM
  • lines changed 6, context: html, text, full: html, text
    8a72f9a35a0cbc73d479bab4d2a17bd8326624b1 Sat Aug 29 13:25:14 2020 -0700
    document interaction between itemRdb and maxItems hub options (#26131)
  • lines changed 1, context: html, text, full: html, text
    508e51bbaa94d79d29b6a25d9e4d55e9783dcb08 Mon Aug 31 06:09:10 2020 -0700
    fixing small typo in markds doc commit
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 46, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
  • lines changed 1, context: html, text, full: html, text
    bf5092e9da71865ab4697719997bb09018b59833 Fri Aug 28 15:54:06 2020 -0700
    Fixing copy error #24524
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    d421969ac452ff392f6f94ef4df46fdb380c7630 Fri Aug 28 12:25:42 2020 -0700
    HTML for gorilla genome releases #24524
• src/hg/htdocs/template.html
  • lines changed 5, context: html, text, full: html, text
    6b728cfec28fbf5e0df8ddfd6cede45a2f120139 Thu Aug 27 14:40:09 2020 -0700
    Fixing errors in template.html discovered in code review by Daniel and Jairo refs #26101
• src/hg/lib/customFactory.c
  • lines changed 21, context: html, text, full: html, text
    02882e0cda463b6bee5f2061eb89b26a437e42e0 Mon Aug 24 12:26:49 2020 -0700
    allow genbank/refseq/ensembl chrom names from chromAlias table for input on bed file custom tracks refs #24396
  • lines changed 1, context: html, text, full: html, text
    57e99ec5381cc522b025ff1259bd27059cc8c19a Tue Aug 25 07:45:19 2020 -0700
    remove debug print statement refs #24396
• src/hg/makeDb/doc/hg19.txt
  • lines changed 5, context: html, text, full: html, text
    15e1169d1ba4e318b78a89bf0e09bbc1d033d950 Mon Aug 24 13:09:18 2020 -0700
    first cut at Franklin display #25405
  • lines changed 6, context: html, text, full: html, text
    aa82ced1f07ddc93917a4e70f269241283cbe84b Tue Aug 25 10:45:34 2020 -0700
    add mouseovers to clinsub
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
  • lines changed 30, context: html, text, full: html, text
    95fe5443b49b71e0f248ca8afccd926e126a4833 Wed Aug 26 18:00:48 2020 -0700
    Updated Problematic Sites track. refs #26126
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 37, context: html, text, full: html, text
    25350394c4a287c6fa6cc6922f58f9bd70be2d50 Fri Aug 28 11:51:07 2020 -0700
    improved description according to new track features refs #24850
  • lines changed 3, context: html, text, full: html, text
    7a90888a6a5f82e890cddf86cc40023771802d75 Fri Aug 28 12:08:50 2020 -0700
    corrected colors SNV variants refs #24850
• src/hg/makeDb/trackDb/human/covidGwas.html
  • lines changed 31, context: html, text, full: html, text
    d93d7b14a11b7c22b2275df5c8db88f9232efeb7 Thu Aug 27 11:00:26 2020 -0700
    First cut COVID GWAS track. refs #26129
  • lines changed 2, context: html, text, full: html, text
    6f6007c432e002ebd3810d905a73c2c607aa4eab Thu Aug 27 11:06:52 2020 -0700
    Fix URLs. refs #26129
• src/hg/makeDb/trackDb/human/covidGwas.ra
  • lines changed 33, context: html, text, full: html, text
    d93d7b14a11b7c22b2275df5c8db88f9232efeb7 Thu Aug 27 11:00:26 2020 -0700
    First cut COVID GWAS track. refs #26129
• src/hg/makeDb/trackDb/human/hg19/clinsub.ra
  • lines changed 12, context: html, text, full: html, text
    15e1169d1ba4e318b78a89bf0e09bbc1d033d950 Mon Aug 24 13:09:18 2020 -0700
    first cut at Franklin display #25405
  • lines changed 1, context: html, text, full: html, text
    aa82ced1f07ddc93917a4e70f269241283cbe84b Tue Aug 25 10:45:34 2020 -0700
    add mouseovers to clinsub
  • lines changed 6, context: html, text, full: html, text
    378370d8c1c61c3d46f870058a0b86200b291fc4 Wed Aug 26 14:46:23 2020 -0700
    use new yLabel syntax
• src/hg/makeDb/trackDb/human/hg38/encodeCcreCombined.html
  • lines changed 9, context: html, text, full: html, text
    f4d738bfa742138640af438a018c82dda683779b Fri Aug 28 10:41:58 2020 -0700
    Adding the ENCODE reference now that it has been published. For hg38 only, mentioning the Roadmap Epigenomics 2015 paper, refs #24668
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra
  • lines changed 1, context: html, text, full: html, text
    7bfa900096eacfa54d1a75a263ab185c903b30e4 Fri Aug 28 10:43:46 2020 -0700
    Turning on the ENCODE cCREs track to 'pack' by default and moving it to the beginning of the Regulation list now that it is a default track. Hiding the DNase Clusters track on hg38 since this track replaces it. refs #24668
• src/hg/makeDb/trackDb/human/trackDb.dbVar.ra
  • lines changed 1, context: html, text, full: html, text
    2902fcdb8a6af9915cd7dffe78068b796150a92f Fri Aug 28 13:06:40 2020 -0700
    changed short track name refs #25424
  • lines changed 28, context: html, text, full: html, text
    555adca1c2689e0dd7dbfe9ac33af162b860be56 Mon Aug 31 09:43:14 2020 -0700
    Turn on search for dbVar track, refs #25424
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    27def01eb26c44ee4fcc4830938f98fb50095c94 Wed Aug 26 16:46:47 2020 -0700
    Staging new clinVar trackDb options on beta, refs #24850
  • lines changed 28, context: html, text, full: html, text
    d93d7b14a11b7c22b2275df5c8db88f9232efeb7 Thu Aug 27 11:00:26 2020 -0700
    First cut COVID GWAS track. refs #26129
• src/hg/makeDb/trackDb/mouse/mm10/encodeCcreCombined.html
  • lines changed 4, context: html, text, full: html, text
    f4d738bfa742138640af438a018c82dda683779b Fri Aug 28 10:41:58 2020 -0700
    Adding the ENCODE reference now that it has been published. For hg38 only, mentioning the Roadmap Epigenomics 2015 paper, refs #24668
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 10, context: html, text, full: html, text
    15e1169d1ba4e318b78a89bf0e09bbc1d033d950 Mon Aug 24 13:09:18 2020 -0700
    first cut at Franklin display #25405
  • lines changed 6, context: html, text, full: html, text
    316f7516c81df7e3827b5e4d60cabb011808b1a5 Wed Aug 26 17:42:14 2020 -0700
    remove yLabel from tagTypes
• src/hg/makeDb/trackDb/trackDb.encode3.ra
  • lines changed 2, context: html, text, full: html, text
    7bfa900096eacfa54d1a75a263ab185c903b30e4 Fri Aug 28 10:43:46 2020 -0700
    Turning on the ENCODE cCREs track to 'pack' by default and moving it to the beginning of the Regulation list now that it is a default track. Hiding the DNase Clusters track on hg38 since this track replaces it. refs #24668
• src/hg/makeDb/trackDb/trackDb.genbank.ra
  • lines changed 1, context: html, text, full: html, text
    a0ffddeb72a81b0a747b46ac46833dd0dc86c412 Wed Aug 26 16:26:55 2020 -0700
    Visibility edits to nextStrainSamples, SARSphylo, pond and mrna tracks refs #25782
• src/hg/makeDb/trackDb/virus/wuhCor1/pond.html
  • lines changed 48, context: html, text, full: html, text
    84671b7a25835087c9dcc3c3b194b4c9feb2baf8 Fri Aug 28 08:08:50 2020 -0700
    Fixing up the desc pages for Nat Selection track refs #25947
• src/hg/makeDb/trackDb/virus/wuhCor1/pond.ra
  • lines changed 1, context: html, text, full: html, text
    a0ffddeb72a81b0a747b46ac46833dd0dc86c412 Wed Aug 26 16:26:55 2020 -0700
    Visibility edits to nextStrainSamples, SARSphylo, pond and mrna tracks refs #25782
  • lines changed 14, context: html, text, full: html, text
    b7ae3fd2d5d46669a80101b46fdca83273ea357c Fri Aug 28 12:49:06 2020 -0700
    Enabling score shading and turning off exon arrows refs #25947
  • lines changed 1, context: html, text, full: html, text
    a6691f8284ad5090ac12d9eb7fc3df61a45dc26d Fri Aug 28 13:35:18 2020 -0700
    Adding pennantIcon to new track refs #25947
• src/hg/makeDb/trackDb/virus/wuhCor1/potPathoIndel.html
  • lines changed 29, context: html, text, full: html, text
    643b11dbf4f45f5acc641db9bed0721f9e509116 Fri Aug 28 05:40:34 2020 -0700
    adding potential pathogenic indels tracks, refs #26132
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
  • lines changed 2, context: html, text, full: html, text
    a0ffddeb72a81b0a747b46ac46833dd0dc86c412 Wed Aug 26 16:26:55 2020 -0700
    Visibility edits to nextStrainSamples, SARSphylo, pond and mrna tracks refs #25782
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a0ffddeb72a81b0a747b46ac46833dd0dc86c412 Wed Aug 26 16:26:55 2020 -0700
    Visibility edits to nextStrainSamples, SARSphylo, pond and mrna tracks refs #25782
  • lines changed 34, context: html, text, full: html, text
    95fe5443b49b71e0f248ca8afccd926e126a4833 Wed Aug 26 18:00:48 2020 -0700
    Updated Problematic Sites track. refs #26126
  • lines changed 7, context: html, text, full: html, text
    643b11dbf4f45f5acc641db9bed0721f9e509116 Fri Aug 28 05:40:34 2020 -0700
    adding potential pathogenic indels tracks, refs #26132
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 3, context: html, text, full: html, text
    19f3bd6bd473e6b5cb3835199c385e7c82329188 Tue Aug 25 12:50:32 2020 -0700
    the -priority option needs to be defined properly for the help message no redmine
• src/hg/utils/automation/chromAliasBedTest.pl
  • lines changed 66, context: html, text, full: html, text
    324671bac877d29cafa50dbc8e944c8c554581aa Mon Aug 24 15:04:28 2020 -0700
    output bed file with every possible name in a database genome refs #24396
  • lines changed 1, context: html, text, full: html, text
    33b5cb286a820d589a23e013a66f8c401c3682bd Tue Aug 25 16:44:36 2020 -0700
    better naming of the alias elements to see their names in the track refs #24396
  • lines changed 5, context: html, text, full: html, text
    3f67e4d0d91bb2f319c9ae26d9dff4eb47990d61 Wed Aug 26 09:14:38 2020 -0700
    must limit name length to under 255 refs #24396
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 30, context: html, text, full: html, text
    653eaa635409806f4885b0486125efd4390c0931 Thu Aug 27 14:00:07 2020 -0700
    fix scripts to behave properly when not using UCSC sequence names refs #23734
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 114, context: html, text, full: html, text
    653eaa635409806f4885b0486125efd4390c0931 Thu Aug 27 14:00:07 2020 -0700
    fix scripts to behave properly when not using UCSC sequence names refs #23734
• src/hg/utils/automation/ncbiRefSeqOtherAttrs.pl
  • lines changed 1, context: html, text, full: html, text
    653eaa635409806f4885b0486125efd4390c0931 Thu Aug 27 14:00:07 2020 -0700
    fix scripts to behave properly when not using UCSC sequence names refs #23734
• src/hg/utils/bedPartition/bedPartition.c
  • lines changed 23, context: html, text, full: html, text
    47a8767ba69ad593d45adb123c189cee3a0f5f85 Thu Aug 27 20:23:01 2020 -0700
    added -partSize option to bedPartition to allow grouping multiple partitions into a range
• src/hg/utils/bedPartition/tests/expected/test2.ranges.bed
  • lines changed 4, context: html, text, full: html, text
    47a8767ba69ad593d45adb123c189cee3a0f5f85 Thu Aug 27 20:23:01 2020 -0700
    added -partSize option to bedPartition to allow grouping multiple partitions into a range
• src/hg/utils/bedPartition/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    47a8767ba69ad593d45adb123c189cee3a0f5f85 Thu Aug 27 20:23:01 2020 -0700
    added -partSize option to bedPartition to allow grouping multiple partitions into a range
• src/hg/utils/otto/decipher/buildDecipher
  • lines changed 1, context: html, text, full: html, text
    c441c8fab1f86d5ffdf876df99ada6adfddd3df9 Thu Aug 27 14:36:52 2020 -0700
    Fixing up uniq command after code review, refs #26100
  • lines changed 0, context: html, text, full: html, text
    af8aad9b9708d958e2efcf46bffd948ae6ac3ba1 Thu Aug 27 14:46:10 2020 -0700
    Fix extraneous whitespace, refs #26100
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 4, context: html, text, full: html, text
    c2a522145128e59acc06adedd08bf9270a207869 Wed Aug 26 14:40:57 2020 -0700
    add yLabel to the set of complex variables that can have a dot after them
• src/utils/chromToUcsc/tests/expected/hg19.bed
  • lines changed 1, context: html, text, full: html, text
    4ffc7b35da25993c19dcfbf60dc952bbf6e2e6b9 Fri Aug 28 09:21:20 2020 -0700
    fixing a chromToUcsc test problem found by the nightly build, no redmine
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    80e8291423b9b56fe7d79f1b4406c53456e1d676 Mon Aug 31 10:00:29 2020 -0700
    v404 preview1

• lines changed: 938
• files changed: 87