File Changes for hiram

v395_preview to v395_preview2 (2020-02-24 to 2020-03-02) v395

• src/hg/bedToGenePred/bedToGenePred.c
  • lines changed 5, context: html, text, full: html, text
    33f43afed02b66b3297e05bde52016292e5325ea Mon Mar 2 09:00:28 2020 -0800
    correct one line header in usage message no redmine
• src/hg/estOrient/estOrient.c
  • lines changed 7, context: html, text, full: html, text
    9c497a369f82a2262cc9767761ae09b04ec5a78d Mon Mar 2 09:06:05 2020 -0800
    correct one line header in usage message no redmine
• src/hg/genePredToBed/genePredToBed.c
  • lines changed 17, context: html, text, full: html, text
    61ba0f65282f7de325bb658bb7862b1338ea9ce1 Fri Feb 28 14:21:19 2020 -0800
    add tab and score options to allow for space in names and to allow score setting refs #23891
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    c6d365fd7d447135c5f167aa5c8898850538729d Fri Feb 28 14:45:11 2020 -0800
    and allow -fillSpace to fixup names with space characters refs #23891
• src/hg/gigAssembler/checkAgpAndFa/checkAgpAndFa.c
  • lines changed 2, context: html, text, full: html, text
    8fb8b7633c8c5f0a7e6657b4d7fb79d6ac96df7b Mon Mar 2 09:02:06 2020 -0800
    correct one line header in usage message no redmine
• src/hg/htdocs/images/SARS-CoV-2.jpg
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    cb8b1cfc8d9435469febb08526e21d7c8b491a83 Fri Feb 28 11:55:47 2020 -0800
    rename virus from 2019-nCoV to SARS-CoV-2, coronavirus viron schematic from Belouzard, et al. Viruses. 2012 Jun; 4(6): 1011-1033 refs #24851
• src/hg/htdocs/images/phylo/danRer10_12way.png
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    23c7550f40be611c0550a0db47d11175289d5988 Wed Feb 26 12:49:28 2020 -0800
    12-way alignment on danRer10 no redmine
• src/hg/js/dbDbTaxonomy.js
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    5d3e45aae48628dc114533005c7b1eb3b9d6cd41 Fri Feb 28 11:50:39 2020 -0800
    rename Wuhan market virus to SARS-CoV-2 refs #24851
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 4, context: html, text, full: html, text
    d3219932529dacd180646575f4892e8a32ba2601 Mon Feb 24 10:16:46 2020 -0800
    adding trackData page construction refs #23891
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 360, context: html, text, full: html, text
    d3219932529dacd180646575f4892e8a32ba2601 Mon Feb 24 10:16:46 2020 -0800
    adding trackData page construction refs #23891
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    32bd9b7bea2ca6154383f124a803fdd6ad04c77b Sat Feb 29 16:41:43 2020 -0800
    add allGaps column and use featureBits result when present and zero when track is empty refs #23891
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
  • lines changed 5, context: html, text, full: html, text
    97cb1f031c965fa01185ce3873c6f856e971c141 Fri Feb 28 11:54:18 2020 -0800
    rename virus from 2019-nCoV to SARS-CoV-2 refs #24851
• src/hg/ratStuff/makefile
  • lines changed 3, context: html, text, full: html, text
    1f25d65e6ccdcb32997ddb28ced16207113e0ac3 Mon Mar 2 07:53:12 2020 -0800
    mafRc is not suitable for a userApp delivery no redmine
• src/hg/utils/automation/asmHubGatewayPage.pl
  • lines changed 12, context: html, text, full: html, text
    186ce9edc8f61d7ad4c8b2e86437a81e29d77ccd Wed Feb 26 14:41:28 2020 -0800
    correctly locate buildDIr with accessionId vs asmId refs #23891
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 8, context: html, text, full: html, text
    81edac3824e0dd89d6cd13e1d668011cd3695ea0 Wed Feb 26 14:44:12 2020 -0800
    begining to function OK for assembly hubs refs #24963
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 56, context: html, text, full: html, text
    66a4bb8eccef8184fe80dbeb638c99f2dcbda169 Wed Feb 26 14:53:01 2020 -0800
    better detection if steps need to be done or have been done or are currently running refs #23891
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    2aa890be7b759af7095a891fa999cb27a63bf5a2 Fri Feb 28 15:32:32 2020 -0800
    better detection if step already done and need to fixup spaces in gene names from NCBI refs #23891
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    97199fbf1ff56c9ee01956deb736b97244ea3ac6 Sun Mar 1 21:52:28 2020 -0800
    calculating featureBits like measurement for gene tracks, removing duplicates for ncbiRefSeq, remove blanks from gene names for ncbiRefSeq, and fix fundamental bug reference to geneToId in ncbiRefSeqOtherAttrs.pl refs #23891
• src/hg/utils/automation/doAugustus.pl
  • lines changed 7, context: html, text, full: html, text
    97199fbf1ff56c9ee01956deb736b97244ea3ac6 Sun Mar 1 21:52:28 2020 -0800
    calculating featureBits like measurement for gene tracks, removing duplicates for ncbiRefSeq, remove blanks from gene names for ncbiRefSeq, and fix fundamental bug reference to geneToId in ncbiRefSeqOtherAttrs.pl refs #23891
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 126, context: html, text, full: html, text
    b63f95d2cb4f728858cb3d63f68e70a234db6db4 Wed Feb 26 14:43:13 2020 -0800
    begining to function OK for assembly hubs refs #24963
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 1, context: html, text, full: html, text
    2aa890be7b759af7095a891fa999cb27a63bf5a2 Fri Feb 28 15:32:32 2020 -0800
    better detection if step already done and need to fixup spaces in gene names from NCBI refs #23891
  • lines changed 15, context: html, text, full: html, text
    97199fbf1ff56c9ee01956deb736b97244ea3ac6 Sun Mar 1 21:52:28 2020 -0800
    calculating featureBits like measurement for gene tracks, removing duplicates for ncbiRefSeq, remove blanks from gene names for ncbiRefSeq, and fix fundamental bug reference to geneToId in ncbiRefSeqOtherAttrs.pl refs #23891
• src/hg/utils/automation/doXenoRefGene.pl
  • lines changed 7, context: html, text, full: html, text
    97199fbf1ff56c9ee01956deb736b97244ea3ac6 Sun Mar 1 21:52:28 2020 -0800
    calculating featureBits like measurement for gene tracks, removing duplicates for ncbiRefSeq, remove blanks from gene names for ncbiRefSeq, and fix fundamental bug reference to geneToId in ncbiRefSeqOtherAttrs.pl refs #23891
• src/hg/utils/automation/makefile
  • lines changed 3, context: html, text, full: html, text
    75778c0fae9df5a460b36ab20cfafd639574534d Wed Feb 26 14:45:15 2020 -0800
    need to deliver kmer functions for doTandenDups script refs #23891
• src/hg/utils/automation/ncbiRefSeqOtherAttrs.pl
  • lines changed 3, context: html, text, full: html, text
    97199fbf1ff56c9ee01956deb736b97244ea3ac6 Sun Mar 1 21:52:28 2020 -0800
    calculating featureBits like measurement for gene tracks, removing duplicates for ncbiRefSeq, remove blanks from gene names for ncbiRefSeq, and fix fundamental bug reference to geneToId in ncbiRefSeqOtherAttrs.pl refs #23891
• src/hg/utils/bedPartition/bedPartition.c
  • lines changed 6, context: html, text, full: html, text
    f22eadf651576744dfe9610b363bcd1a8161334c Mon Mar 2 08:58:53 2020 -0800
    correct one line header in usage message no redmine
• src/utils/bedJoinTabOffset/bedJoinTabOffset.c
  • lines changed 1, context: html, text, full: html, text
    6f796d7565a982f9b94cd3a0632aacc0c6abc3e1 Mon Mar 2 08:53:52 2020 -0800
    correct one line header to usage message no redmine