All File Changes

v394_base to v395_preview (2020-02-17 to 2020-02-24) v395

• confs/hgwdev.hg.conf
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    3899a4e476d5d132f4a0d314a4914bd65c21fe4c Sun Feb 23 01:11:41 2020 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/cescg/cescgPeople.html
  • lines changed 1, context: html, text, full: html, text
    4887faf0a1131bc32a604c46eba59a3ebdd08f25 Wed Feb 19 07:51:21 2020 -0800
    Fixed name: kameron -> kamron
• src/hg/featureBits/featureBits.c
  • lines changed 4, context: html, text, full: html, text
    77421e0dc5eb5327b15ce1d12509d549068dfc73 Thu Feb 20 10:48:31 2020 -0800
    featureBits .chain support: ignore chains on chroms other than the current chrom, and lineFileClose when done. tangentially refs #21650
• src/hg/hgBlat/hgBlat.c
  • lines changed 4, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/hgCustom/hgCustom.c
  • lines changed 6, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/hgGene/hgGene.c
  • lines changed 2, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/hgTables/bigBed.c
  • lines changed 42, context: html, text, full: html, text
    d1a11e955077906d793c5f6ca9eee3c40a77f1b0 Wed Feb 19 14:24:48 2020 -0800
    use a name index in a bigBed if available and there are identifiers in hgTables and the region is whole genome
• src/hg/hgTables/hgTables.c
  • lines changed 28, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
  • lines changed 14, context: html, text, full: html, text
    d1a11e955077906d793c5f6ca9eee3c40a77f1b0 Wed Feb 19 14:24:48 2020 -0800
    use a name index in a bigBed if available and there are identifiers in hgTables and the region is whole genome
• src/hg/hgTables/hgTables.h
  • lines changed 3, context: html, text, full: html, text
    d1a11e955077906d793c5f6ca9eee3c40a77f1b0 Wed Feb 19 14:24:48 2020 -0800
    use a name index in a bigBed if available and there are identifiers in hgTables and the region is whole genome
• src/hg/hgTables/hic.c
  • lines changed 1, context: html, text, full: html, text
    8fbe3d525f15c3f5090d9ad67aa90d6f3df2bdd3 Wed Feb 19 10:49:13 2020 -0800
    Fixing malformed tableInfo for converting hic to BED. Should be bed3, not bed5. refs #24988
• src/hg/hgTables/schema.c
  • lines changed 8, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/hgTracks/hgTracks.c
  • lines changed 20, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/hgTracks/pslTrack.c
  • lines changed 125, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 16, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/hgc/hgc.c
  • lines changed 59, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 2, context: html, text, full: html, text
    fa8b8585e87d433f26deca1d476b122f1425ca96 Wed Feb 19 13:59:44 2020 -0800
    added some hyphens where needed
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 20, context: html, text, full: html, text
    45b9a4913c541df94db2c172896fe26668a43a26 Wed Feb 19 14:10:26 2020 -0800
    Documenting validate hub feature #24429
  • lines changed 3, context: html, text, full: html, text
    6222dbdb62ec9564c14b39dd580145b64e7a5a6a Wed Feb 19 14:16:29 2020 -0800
    Documenting validate hub feature, edit #24429
  • lines changed 7, context: html, text, full: html, text
    22a4ecd91a6aa015b9a8807b9c2c883c962ff694 Wed Feb 19 14:48:27 2020 -0800
    Documenting validate hub feature, edit2 #24429
  • lines changed 1, context: html, text, full: html, text
    226cd00ff731dccba8b7a5a75be4a823f0d4a39a Wed Feb 19 15:13:16 2020 -0800
    Documenting validate hub feature, edit3 #24429
  • lines changed 1, context: html, text, full: html, text
    67d8b9526535b1bbb93cd03b2b085958670c9557 Thu Feb 20 16:04:40 2020 -0800
    Code Review change refs #24985
• src/hg/htdocs/images/validateHub.png
  • lines changed 0, context: html, text, full: html, text
    45b9a4913c541df94db2c172896fe26668a43a26 Wed Feb 19 14:10:26 2020 -0800
    Documenting validate hub feature #24429
• src/hg/inc/hCommon.h
  • lines changed 12, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/lib/cart.c
  • lines changed 135, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/lib/hCommon.c
  • lines changed 44, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    b007d488929cf1fbccead6e92cee1fe7464a10d5 Fri Feb 14 03:34:38 2020 -0800
    uppercasing links on trackui pages, refs #24372
  • lines changed 57, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/lib/validateGisaid.c
  • lines changed 21, context: html, text, full: html, text
    3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515 Mon Feb 17 10:41:18 2020 -0800
    delete long unused code for HIV, Cancer browser. RIP Fan.
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 12, context: html, text, full: html, text
    22a9ec8b34dd60a14257bdef408f21c03db601b4 Mon Feb 17 16:06:38 2020 -0800
    now using the shorter assembly name for genome identifier and fix some common names refs #23891
• src/hg/makeDb/doc/asmHubs/makefile
  • lines changed 37, context: html, text, full: html, text
    22a9ec8b34dd60a14257bdef408f21c03db601b4 Mon Feb 17 16:06:38 2020 -0800
    now using the shorter assembly name for genome identifier and fix some common names refs #23891
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 2, context: html, text, full: html, text
    22a9ec8b34dd60a14257bdef408f21c03db601b4 Mon Feb 17 16:06:38 2020 -0800
    now using the shorter assembly name for genome identifier and fix some common names refs #23891
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 6, context: html, text, full: html, text
    22a9ec8b34dd60a14257bdef408f21c03db601b4 Mon Feb 17 16:06:38 2020 -0800
    now using the shorter assembly name for genome identifier and fix some common names refs #23891
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 3, context: html, text, full: html, text
    22a9ec8b34dd60a14257bdef408f21c03db601b4 Mon Feb 17 16:06:38 2020 -0800
    now using the shorter assembly name for genome identifier and fix some common names refs #23891
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 5, context: html, text, full: html, text
    22a9ec8b34dd60a14257bdef408f21c03db601b4 Mon Feb 17 16:06:38 2020 -0800
    now using the shorter assembly name for genome identifier and fix some common names refs #23891
• src/hg/makeDb/doc/birdsAsmHub/makefile
  • lines changed 2, context: html, text, full: html, text
    0503f0e3879f41dda5a9e6b807dd948fe910d745 Mon Feb 17 16:08:41 2020 -0800
    now using the shorter assembly identifer for genome name refs #23891
• src/hg/makeDb/doc/fishAsmHub/makefile
  • lines changed 2, context: html, text, full: html, text
    0503f0e3879f41dda5a9e6b807dd948fe910d745 Mon Feb 17 16:08:41 2020 -0800
    now using the shorter assembly identifer for genome name refs #23891
• src/hg/makeDb/doc/hg19.addChrMT.txt
  • lines changed 16, context: html, text, full: html, text
    f7d9c08f80220550ac2f58cbb9e17e957c5f3e51 Wed Feb 19 09:35:46 2020 -0800
    hg19 uses gc5Base not gc5BaseBw -- add p13 + chrMT data to gc5Base. refs #24648
  • lines changed 76, context: html, text, full: html, text
    4deb0c9ffddc09de17d71a387cec95c9a1cbfc14 Thu Feb 20 11:30:48 2020 -0800
    Oops, need to ensure sortedness of db tables after adding patch sequences - thx Jairo. refs #24648
• src/hg/makeDb/doc/hg38/patchUpdate.12.txt
  • lines changed 5, context: html, text, full: html, text
    4deb0c9ffddc09de17d71a387cec95c9a1cbfc14 Thu Feb 20 11:30:48 2020 -0800
    Oops, need to ensure sortedness of db tables after adding patch sequences - thx Jairo. refs #24648
• src/hg/makeDb/doc/mammalsAsmHub/hub.txt
  • lines changed 3, context: html, text, full: html, text
    b453f8b92536b6c2280d2f02dc45150fc2d4cbcb Mon Feb 17 16:13:56 2020 -0800
    correct name for this hub.txt refs #23891
• src/hg/makeDb/doc/mammalsAsmHub/makefile
  • lines changed 3, context: html, text, full: html, text
    0503f0e3879f41dda5a9e6b807dd948fe910d745 Mon Feb 17 16:08:41 2020 -0800
    now using the shorter assembly identifer for genome name refs #23891
• src/hg/makeDb/doc/primatesAsmHub/hub.txt
  • lines changed 1, context: html, text, full: html, text
    e576244638baffc0950375f9f7c14a392e93b193 Mon Feb 17 16:14:24 2020 -0800
    correct name for this hub.txt refs #23891
• src/hg/makeDb/doc/primatesAsmHub/makefile
  • lines changed 3, context: html, text, full: html, text
    0503f0e3879f41dda5a9e6b807dd948fe910d745 Mon Feb 17 16:08:41 2020 -0800
    now using the shorter assembly identifer for genome name refs #23891
• src/hg/makeDb/doc/vertebrateAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    b8652889568318e20760075bc46291560f93026a Mon Feb 17 16:07:32 2020 -0800
    using the shorter makefile procedure refs #23891
• src/hg/makeDb/doc/vertebrateAsmHub/makefile
  • lines changed 9, context: html, text, full: html, text
    b8652889568318e20760075bc46291560f93026a Mon Feb 17 16:07:32 2020 -0800
    using the shorter makefile procedure refs #23891
• src/hg/makeDb/doc/vertebrateAsmHub/mkList.sh
  • lines changed 28, context: html, text, full: html, text
    b8652889568318e20760075bc46291560f93026a Mon Feb 17 16:07:32 2020 -0800
    using the shorter makefile procedure refs #23891
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.taxId.list
  • lines changed 29, context: html, text, full: html, text
    b8652889568318e20760075bc46291560f93026a Mon Feb 17 16:07:32 2020 -0800
    using the shorter makefile procedure refs #23891
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.xrefName.list
  • lines changed 26, context: html, text, full: html, text
    b8652889568318e20760075bc46291560f93026a Mon Feb 17 16:07:32 2020 -0800
    using the shorter makefile procedure refs #23891
• src/hg/makeDb/doc/vertebratesAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    ea52f7b77dacc8394101c6d841fcb845eec488c6 Mon Feb 17 16:11:16 2020 -0800
    moved to vertebrateAsmHub refs #23891
• src/hg/makeDb/doc/vertebratesAsmHub/makefile
  • lines changed 8, context: html, text, full: html, text
    ea52f7b77dacc8394101c6d841fcb845eec488c6 Mon Feb 17 16:11:16 2020 -0800
    moved to vertebrateAsmHub refs #23891
• src/hg/makeDb/doc/vertebratesAsmHub/mkList.sh
  • lines changed 28, context: html, text, full: html, text
    ea52f7b77dacc8394101c6d841fcb845eec488c6 Mon Feb 17 16:11:16 2020 -0800
    moved to vertebrateAsmHub refs #23891
• src/hg/makeDb/doc/vertebratesAsmHub/vertebrate.taxId.list
  • lines changed 29, context: html, text, full: html, text
    ea52f7b77dacc8394101c6d841fcb845eec488c6 Mon Feb 17 16:11:16 2020 -0800
    moved to vertebrateAsmHub refs #23891
• src/hg/makeDb/doc/vertebratesAsmHub/vertebrate.xrefName.list
  • lines changed 26, context: html, text, full: html, text
    ea52f7b77dacc8394101c6d841fcb845eec488c6 Mon Feb 17 16:11:16 2020 -0800
    moved to vertebrateAsmHub refs #23891
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    57ed99f0e1f214297c25ff6cfa5f512bff7e8f0b Fri Feb 21 13:59:53 2020 -0800
    Adding refseq select to all.joiner refs #24787
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
  • lines changed 1, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/human/hg16/description.html
  • lines changed 4, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/human/hg17/description.html
  • lines changed 4, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/human/hg18/description.html
  • lines changed 4, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 2, context: html, text, full: html, text
    6c6c63f5091b8c69b160cca12b046146494d21be Fri Feb 21 14:15:14 2020 -0800
    Removing release tags on DGV track now converted to a bigBed to use filters refs #24749
• src/hg/makeDb/trackDb/human/hg19/gnomadPLI.html
  • lines changed 29, context: html, text, full: html, text
    4a5eb5bf96cd5700bbd922b3b703959425868e37 Mon Feb 17 14:45:06 2020 -0800
    Polishing gnomAD Predicted Loss of Function track description page refs #20394
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 1, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    6c6c63f5091b8c69b160cca12b046146494d21be Fri Feb 21 14:15:14 2020 -0800
    Removing release tags on DGV track now converted to a bigBed to use filters refs #24749
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 30, context: html, text, full: html, text
    abbbd616fe0c3203b35cae02fc2f8b063c3b1d9c Wed Feb 19 14:12:44 2020 -0800
    converting clinvar to two files that are included, refs #24850
• src/hg/makeDb/trackDb/human/trackDb.clinvarTest.ra
  • lines changed 42, context: html, text, full: html, text
    abbbd616fe0c3203b35cae02fc2f8b063c3b1d9c Wed Feb 19 14:12:44 2020 -0800
    converting clinvar to two files that are included, refs #24850
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 47, context: html, text, full: html, text
    abbbd616fe0c3203b35cae02fc2f8b063c3b1d9c Wed Feb 19 14:12:44 2020 -0800
    converting clinvar to two files that are included, refs #24850
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • lines changed 1, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/medaka/oryLat1/description.html
  • lines changed 1, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/microbat/myoLuc2/description.html
  • lines changed 1, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/pig/susScr2/description.html
  • lines changed 1, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 12, context: html, text, full: html, text
    401476f97d2e31e0880a181adffea05aad28996c Tue Feb 18 16:16:06 2020 -0800
    Clarifying name of RefSeq Select/MANE and expanding track description page refs #24787
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 2, context: html, text, full: html, text
    401476f97d2e31e0880a181adffea05aad28996c Tue Feb 18 16:16:06 2020 -0800
    Clarifying name of RefSeq Select/MANE and expanding track description page refs #24787
  • lines changed 1, context: html, text, full: html, text
    5fa80aa43fc0ca5733041769071a9e63a35a3966 Tue Feb 18 16:18:27 2020 -0800
    Fixing up stragler in MANE/Select clarification refs #24787
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
  • lines changed 2, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/turkey/melGal1/description.html
  • lines changed 1, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
  • lines changed 1, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/worm/caeAng2/description.html
  • lines changed 1, context: html, text, full: html, text
    c6d77348dec9ec45ba61c97a0840ae2301d0fe7c Fri Feb 21 15:02:20 2020 -0800
    Fixing broken links in description pages #24754
• src/hg/makeDb/trackDb/zebrafish/danRer3/rhMap.html
  • lines changed 1, context: html, text, full: html, text
    08fdb11b7a627f16af03f5bb5a70d11361c90949 Wed Feb 19 09:12:33 2020 -0800
    Updating http to https for danRer3, uiLinks cronjob
• src/hg/utils/automation/asmHubEnsGene.pl
  • lines changed 5, context: html, text, full: html, text
    53d682e17e5ae17bd10a2f240178d05b4da9d0f4 Mon Feb 17 16:39:15 2020 -0800
    correct behavior for trackDb for ensGene track refs #23891
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 17, context: html, text, full: html, text
    53d682e17e5ae17bd10a2f240178d05b4da9d0f4 Mon Feb 17 16:39:15 2020 -0800
    correct behavior for trackDb for ensGene track refs #23891
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 4, context: html, text, full: html, text
    ecc8358a1e03a67aba51417799cca013f98eacc5 Mon Feb 17 16:38:17 2020 -0800
    correct construction of name index file from the gtfToGenePred infoOut.txt newer format refs #23891
• src/hg/utils/genePredFilter/genePredFilter.c
  • lines changed 14, context: html, text, full: html, text
    ea8b0592fa84d8ea6a69ab9036609b4bdad4bd29 Tue Feb 18 15:12:25 2020 -0800
    need to have this genePredFilter do the elimination of illegal itesm instead of hgLoadGenePred for assembly hub track construction refs #24963
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 23, context: html, text, full: html, text
    800312e66545e7d7fd4805c99717bd32c4b47c33 Tue Feb 18 16:49:45 2020 -0800
    Fixing spurious newline stripping in hubCheck. When checking a subGroupN line for a composite track, a warn is thrown and hubCheck continues, if a single stanza has multiple cases of bad subGroups, then all these warning messages were stuck together and not being printed correctly, refs #24958
  • lines changed 34, context: html, text, full: html, text
    bcaf231f7de3921efe6814afe820e1ba4b1e1be0 Wed Feb 19 11:55:53 2020 -0800
    Adding a test for missing hub description or genome description pages, refs #13428
  • lines changed 40, context: html, text, full: html, text
    5b16886cc31572cdab8c383bfbdd2ad60de13617 Thu Feb 20 14:15:01 2020 -0800
    Fixups to hubCheck html option so that checking for hub description page and genome description pages works, refs #24958
  • lines changed 7, context: html, text, full: html, text
    db063154dcf9c02922ff4b94922d713c2bbb5f4c Fri Feb 21 16:37:35 2020 -0800
    Don't use udc to check for existence of hub description pages unless the file is a local file. The polytracts hub does not return a Content-Length header for the hub description page so even though it exists udcExists() doesn't find it, refs Lou email
• src/hg/utils/hubCheck/tests/expected/manyErrors.output.txt
  • lines changed 2, context: html, text, full: html, text
    800312e66545e7d7fd4805c99717bd32c4b47c33 Tue Feb 18 16:49:45 2020 -0800
    Fixing spurious newline stripping in hubCheck. When checking a subGroupN line for a composite track, a warn is thrown and hubCheck continues, if a single stanza has multiple cases of bad subGroups, then all these warning messages were stuck together and not being printed correctly, refs #24958
  • lines changed 2, context: html, text, full: html, text
    bcaf231f7de3921efe6814afe820e1ba4b1e1be0 Wed Feb 19 11:55:53 2020 -0800
    Adding a test for missing hub description or genome description pages, refs #13428
• src/hg/utils/hubCheck/tests/expected/output1.txt
  • lines changed 3, context: html, text, full: html, text
    bcaf231f7de3921efe6814afe820e1ba4b1e1be0 Wed Feb 19 11:55:53 2020 -0800
    Adding a test for missing hub description or genome description pages, refs #13428
  • lines changed 2, context: html, text, full: html, text
    5b16886cc31572cdab8c383bfbdd2ad60de13617 Thu Feb 20 14:15:01 2020 -0800
    Fixups to hubCheck html option so that checking for hub description page and genome description pages works, refs #24958
• src/hg/utils/hubCheck/tests/expected/output2.txt
  • lines changed 2, context: html, text, full: html, text
    5b16886cc31572cdab8c383bfbdd2ad60de13617 Thu Feb 20 14:15:01 2020 -0800
    Fixups to hubCheck html option so that checking for hub description page and genome description pages works, refs #24958
• src/hg/utils/hubCheck/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    bcaf231f7de3921efe6814afe820e1ba4b1e1be0 Wed Feb 19 11:55:53 2020 -0800
    Adding a test for missing hub description or genome description pages, refs #13428
• src/inc/common.h
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    b8a1d025b9e09702debcf84cd656be0cf8032a62 Thu Feb 20 11:46:12 2020 -0800
    work around a problem with %g going into scientific notation too early
• src/inc/hash.h
  • lines changed 3, context: html, text, full: html, text
    d1a11e955077906d793c5f6ca9eee3c40a77f1b0 Wed Feb 19 14:24:48 2020 -0800
    use a name index in a bigBed if available and there are identifiers in hgTables and the region is whole genome
• src/lib/cheapcgi.c
  • lines changed 4, context: html, text, full: html, text
    b8a1d025b9e09702debcf84cd656be0cf8032a62 Thu Feb 20 11:46:12 2020 -0800
    work around a problem with %g going into scientific notation too early
• src/lib/common.c
  • lines changed 13, context: html, text, full: html, text
    b8a1d025b9e09702debcf84cd656be0cf8032a62 Thu Feb 20 11:46:12 2020 -0800
    work around a problem with %g going into scientific notation too early
• src/lib/hash.c
  • lines changed 13, context: html, text, full: html, text
    d1a11e955077906d793c5f6ca9eee3c40a77f1b0 Wed Feb 19 14:24:48 2020 -0800
    use a name index in a bigBed if available and there are identifiers in hgTables and the region is whole genome
• src/product/ex.hg.conf
  • lines changed 4, context: html, text, full: html, text
    e974e46d75d40bcb0bed9e23282cf897c038ab04 Thu Feb 20 18:04:34 2020 -0800
    Documenting hub validator in example hg.conf
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    b85eb92f23847fc1076ded2077f1a94303bd37a9 Mon Feb 24 10:03:32 2020 -0800
    v395 preview1, refs #24908

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• files changed: 102