All File Changes

v400_preview2 to v400_base (2020-06-15 to 2020-06-22) v400

• confs/asia.hg.conf
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    c637736846e10107fe3e70b3dcc6fd8e8e79710f Sun Jun 21 01:11:43 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    c637736846e10107fe3e70b3dcc6fd8e8e79710f Sun Jun 21 01:11:43 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
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    c637736846e10107fe3e70b3dcc6fd8e8e79710f Sun Jun 21 01:11:43 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/blat/version.doc
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    9aa8cb048fd8b72bb544b78d335dee347e8c207f Wed Jun 17 15:29:29 2020 -0700
    Increment blat version number. Now we konw if blat version is 36x7 or newer, the compiler optimization bug should be fixed. refs #25700
• src/hg/hgGene2/assoc.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/hgGene2/assoc.h
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/hgGene2/hgGene2.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/hgTracks/hgTracks.c
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    0cd5f4b2378530681f734607a53392ad19e34156 Mon Jun 22 09:02:45 2020 -0700
    Revert change to caps on go button, which makes it inconsistent with all other buttons on page.
• src/hg/hgTracks/simpleTracks.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
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    138c9fcee4159430e9652c28e2e9b0390e412454 Tue Jun 16 13:13:50 2020 -0700
    remove dependency on kgXref if using a bigGenePred file for UCSC genes
• src/hg/hgTracks/vcfTrack.c
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    8d9367da0e57755641dbbf6498093f7e44f14f12 Sat Jun 20 13:27:08 2020 -0700
    VCF: support up to 64k genotypes, including haplotype+tree display. sorta refs #25278 The VCF parser currently has a hardcoded upper limit on the number of genotype columns. I increased that from 16k to 64k to support Rob Lanfear's SARS-CoV-2 tree w/40k nodes. It will keep growing, so I will probably want to revisit so that we allocate the array size needed instead of a hardcoded huge size when most VCF tracks don't have anywhere near that many. In vcfTracks.c, using 'unsigned short' for the gtHapOrder array limits the number of samples to 32k because the index into gtHapOrder is gtIx<<1+hapIx. Changed all the shorts to ints because we now have VCF with more than 32k genotype columns.
• src/hg/hgc/hgc.c
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    3f1b7b784bc29576d0661e0041f3167c3cbe3483 Mon Jun 22 03:05:26 2020 -0700
    allowing extra fields refered in urls tdb statement to be full URLs without a label, no redmine yet, email from Chris Lee to browser-staff
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    7f5722b3712324de253ab8223d40ff1b10c10ee9 Mon Jun 22 07:31:12 2020 -0700
    adding support for the name omimGene2bb to the omimGene2 hgc handler. refs #18419
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 28, context: html, text, full: html, text
    c8b2bf8f976f6a8ed4c66cb5402e8ae1ab2436f0 Fri Jun 19 14:29:42 2020 -0700
    Remove carelessly duped section. refs #25753
• src/hg/htdocs/goldenPath/newsarch.html
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    38efe73ca469fb8bff5206559a713488a4561ba0 Thu Jun 18 16:25:41 2020 -0700
    Adding the announcement for the ENCODE cCREs track for human and mouse, refs #24668
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    d052043384f869056aa55296e967077b9afb5970 Thu Jun 18 16:58:38 2020 -0700
    Releasing updated chain self tracks refs #24695
• src/hg/htdocs/images/announcement_06182020.png
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    bf403ddd94c9dc72dfd5de3fab2a38d13b068111 Wed Jun 17 16:50:15 2020 -0700
    Adding a browser image for the ENCODE cCRE announcement, refs #24668
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    474950462f28d624254f52a4919e499475d53220 Thu Jun 18 14:36:13 2020 -0700
    Replacing the ENCODE cCREs track image for the announcement, refs #24668
• src/hg/htdocs/images/ccreAnnouncementScreenshot.png
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    474950462f28d624254f52a4919e499475d53220 Thu Jun 18 14:36:13 2020 -0700
    Replacing the ENCODE cCREs track image for the announcement, refs #24668
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    d052043384f869056aa55296e967077b9afb5970 Thu Jun 18 16:58:38 2020 -0700
    Releasing updated chain self tracks refs #24695
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    db3644702473b8f7bf9fb85daf60477e58731f23 Fri Jun 19 14:55:55 2020 -0700
    Adding an entry to the indexNews.html page, refs #24668
• src/hg/htdocs/style/HGStyle.css
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    00b21d2de7388993df52cfdb445b5d6e15c6a9f2 Wed Jun 17 20:02:10 2020 -0700
    change OMIM table background color refs #18419
• src/hg/inc/gencodeAnnotationRemark.h
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeAttrs.h
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeExonSupport.h
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeGeneSource.h
  • lines changed 64, context: html, text, full: html, text
    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeTag.h
  • lines changed 64, context: html, text, full: html, text
    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeToEntrezGene.h
  • lines changed 64, context: html, text, full: html, text
    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeToGeneSymbol.h
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeToPdb.h
  • lines changed 64, context: html, text, full: html, text
    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeToPubMed.h
  • lines changed 64, context: html, text, full: html, text
    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeToRefSeq.h
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeToUniProt.h
  • lines changed 71, context: html, text, full: html, text
    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeTranscriptSource.h
  • lines changed 64, context: html, text, full: html, text
    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeTranscriptSupport.h
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/gencodeTranscriptionSupportLevel.h
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/inc/versionInfo.h
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    e24be750c2eaaeb78ed10b81b44471b19476c6c1 Mon Jun 22 09:58:57 2020 -0700
    New version number v400
• src/hg/lib/gencodeAnnotationRemark.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeAnnotationRemark.c
  • lines changed 126, context: html, text, full: html, text
    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeAnnotationRemark.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeAttrs.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeAttrs.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeAttrs.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeExonSupport.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeExonSupport.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeExonSupport.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeGeneSource.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeGeneSource.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeGeneSource.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTag.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTag.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTag.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToEntrezGene.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToEntrezGene.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToEntrezGene.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToGeneSymbol.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToGeneSymbol.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToGeneSymbol.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToPdb.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToPdb.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToPdb.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToPubMed.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToPubMed.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToPubMed.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToRefSeq.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToRefSeq.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToRefSeq.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToUniProt.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToUniProt.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeToUniProt.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTranscriptSource.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTranscriptSource.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTranscriptSource.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTranscriptSupport.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTranscriptSupport.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTranscriptSupport.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTranscriptionSupportLevel.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTranscriptionSupportLevel.c
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/gencodeTranscriptionSupportLevel.sql
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/hdb.c
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    9c20ec91f0ecd76e8fad18fa0e381c8be894236b Thu Jun 18 12:35:00 2020 -0700
    if the trackDb table has changed in the last five minutes, avoid caching because the table may not be done changing. Updates are not atomic.
• src/hg/lib/htmlTables.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/makefile
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/lib/mergedBGP.as
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/doc/ambMex2/initialBuild.txt
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    c15d38611d858377a05366fd11f507f4dbf90cac Fri Jun 19 10:51:55 2020 -0700
    trying to get masking done with a special library refs #23367
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
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    0c6145f99f76da49d5bbed9d2e775bb5a619c2ab Wed Jun 17 14:08:34 2020 -0700
    no need to sed names now that commonHtml.pm is used refs #25555
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    1a40e3021a59b8139fd74aa9aa6cc0146e6273d8 Fri Jun 19 09:06:35 2020 -0700
    now using unique hub.txt files for each subset refs #25555
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
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    982d69ac4a666c4ff32f7ed167f788b81d960285 Wed Jun 17 12:30:05 2020 -0700
    reduce the vertical space consumed by options and explanations refs #25555
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
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    982d69ac4a666c4ff32f7ed167f788b81d960285 Wed Jun 17 12:30:05 2020 -0700
    reduce the vertical space consumed by options and explanations refs #25555
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• src/hg/makeDb/outside/gencode/tests/expected/ummappingWarnHs38Test.out
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/expected/ummappingWarnHs38Test.unmapped.gp
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/input/examples1.Exon_supporting_feature
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/input/mappingErrorsHs38.gtf
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/input/set1.gtf
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/input/specialCases1.gtf
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/input/tags.gff3
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
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• src/hg/makeDb/outside/gencode/tests/input/tags.gtf
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
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• src/hg/makeDb/outside/gencode/tests/input/v19.gtf
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/input/v21.gff3
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/input/v21.gtf
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/input/v27.par.gff3
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/input/v27.par.gtf
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/outside/gencode/tests/makefile
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
• src/hg/makeDb/schema/all.joiner
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    a35f450f1d4f1f128460141ab8e8faea28980fe6 Mon Jun 15 10:35:08 2020 -0700
    adding rules for panPan3 refs #25720
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
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    4e7d82cb16cd4cea93698834b637815cd74c7960 Mon Jun 15 17:35:53 2020 -0700
    adding definitions for panPan3 chainNet refs #25720
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    a3c14fb7b09c470918286385c0351f3786d7d48e Fri Jun 19 13:13:19 2020 -0700
    Fixing up some clingen related filters and urls, refs #25562
• src/hg/makeDb/trackDb/human/hg38/encodeCcreCombined.html
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    faedd2e68650065d719bc2bb158ce87039bf0731 Wed Jun 17 17:06:57 2020 -0700
    Removing an extra column from the display and conventions table, refs #24668
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.ra
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    fab8cac29e64fd954e034c88245ce20ed3f64e3a Wed Jun 17 17:00:01 2020 -0700
    Updating and releasing MANE v.9 refs #25665
• src/hg/makeDb/trackDb/human/hg38/mane.html
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    fab8cac29e64fd954e034c88245ce20ed3f64e3a Wed Jun 17 17:00:01 2020 -0700
    Updating and releasing MANE v.9 refs #25665
• src/hg/makeDb/trackDb/human/hg38/mane.ra
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    fab8cac29e64fd954e034c88245ce20ed3f64e3a Wed Jun 17 17:00:01 2020 -0700
    Updating and releasing MANE v.9 refs #25665
• src/hg/makeDb/trackDb/human/hg38/mergedBGP.ra
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
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    dbf814664e8400296fb98c1b7d30c7f09e685809 Tue Jun 16 06:53:09 2020 -0700
    temp fix to merge genes
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    c97db9f0a5f3c6d03d63042130e5919ec3542226 Tue Jun 16 09:42:48 2020 -0700
    oops.. a couple of other things the world isn't ready for yet
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
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    c652620bda844fbae173f22e801d5935f5d24c98 Tue Jun 16 10:08:35 2020 -0700
    Need valid chromosome list in the parent stanza for trio composite, refs #25582
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    fab8cac29e64fd954e034c88245ce20ed3f64e3a Wed Jun 17 17:00:01 2020 -0700
    Updating and releasing MANE v.9 refs #25665
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    a3c14fb7b09c470918286385c0351f3786d7d48e Fri Jun 19 13:13:19 2020 -0700
    Fixing up some clingen related filters and urls, refs #25562
• src/hg/makeDb/trackDb/human/omimDescriptionText.html
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    18015d0223dafa5a895098ccf89f5ca1f03c8742 Wed Jun 17 13:18:14 2020 -0700
    corrected OMIM track names refs #25682
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
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    6a19fa2bf0a5cc04ccccbaf87fd2838d1dd2b9f9 Tue Jun 16 11:01:29 2020 -0700
    added (ClinGen) to track long names refs #25562
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    a3c14fb7b09c470918286385c0351f3786d7d48e Fri Jun 19 13:13:19 2020 -0700
    Fixing up some clingen related filters and urls, refs #25562
• src/hg/makeDb/trackDb/human/trackDb.ra
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    218763c25725af6349f5ee728d402b616b00850b Tue Jun 16 11:52:07 2020 -0700
    standarized short and long names of omim tracks refs #25682
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    0a45e7d2edcc6354192a406f61c8f1a22565011a Wed Jun 17 13:05:42 2020 -0700
    corrected spelling in OMIM alelles track long name refs #25682
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
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    dcb18df764920fcb7a6fb9fd1e3380a9bb86d3d7 Wed Jun 17 09:34:15 2020 -0700
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/marmoset/calJac1/nscanGene.html
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    dcb18df764920fcb7a6fb9fd1e3380a9bb86d3d7 Wed Jun 17 09:34:15 2020 -0700
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm10/encodeCcreCombined.html
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    faedd2e68650065d719bc2bb158ce87039bf0731 Wed Jun 17 17:06:57 2020 -0700
    Removing an extra column from the display and conventions table, refs #24668
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
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    4e7d82cb16cd4cea93698834b637815cd74c7960 Mon Jun 15 17:35:53 2020 -0700
    adding definitions for panPan3 chainNet refs #25720
• src/hg/makeDb/trackDb/trackDb.encode3.ra
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    be9f46a390b415cd98b7181adc7ef8b18bda30ee Fri Jun 19 14:20:21 2020 -0700
    Adding the pennantIcon for the ENCODE cCREs track for human and mouse, refs #24668
• src/hg/makeDb/trackDb/virus/wuhCor1/addgene.html
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    f2869e20a6b770952fa18141f0592548792bba81 Thu Jun 18 17:42:23 2020 -0700
    Fixing up trackDb and desc page for the addgene plasmids track refs #25683
• src/hg/makeDb/trackDb/virus/wuhCor1/addgene.ra
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    f2869e20a6b770952fa18141f0592548792bba81 Thu Jun 18 17:42:23 2020 -0700
    Fixing up trackDb and desc page for the addgene plasmids track refs #25683
• src/hg/makeDb/trackDb/virus/wuhCor1/cons7way.html
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    533b80bf457727da3559f7bbf02394db14278f40 Wed Jun 17 15:58:25 2020 -0700
    Clarified and edited for #25609
• src/hg/makeDb/trackDb/virus/wuhCor1/microdel.html
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    26db3dee573c833efa100502dbad4564ab59f1ab Wed Jun 17 02:55:49 2020 -0700
    microdeletion track docs page, refs #25609
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.7way.ra
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    c1652ce0c3eb547b499bb530f27228b6cbd4607b Wed Jun 17 14:23:22 2020 -0700
    eliminate useless views and references to phyloP phastCons mostConserved refs #25569
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    528badcefb8bd80c1f3bb8a421b9ad2f4c0c6db7 Thu Jun 18 16:38:56 2020 -0700
    Adding pennantIcon #25569
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    e314c3c928a6aad0a180b0b1b26047399bf414b2 Tue Jun 16 14:46:06 2020 -0700
    Adding the missing track description page to the composite and subtracks, refs #25708
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    c5c91e99b2c06c5b41279241e3a5a496c1c67183 Wed Jun 17 08:48:23 2020 -0700
    Added the wrong html page to the Nanopore Coverage track. refs #25708
• src/hg/makefile
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    95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700
    Merging in our gencode merge code to master branch
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    a073bb760b58adfe68dc9bf28efdfef778baedb3 Tue Jun 16 08:29:49 2020 -0700
    remove hgGene2 from makefile
• src/hg/oneShot/tfydToRa/README.txt
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    711770a0ca29d71d2ce8227a787be163f05f577d Wed Jun 17 05:24:30 2020 -0700
    adding trackDb for your data hub static html converter to ra format, refs #25745
• src/hg/oneShot/tfydToRa/tfydToRa
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    711770a0ca29d71d2ce8227a787be163f05f577d Wed Jun 17 05:24:30 2020 -0700
    adding trackDb for your data hub static html converter to ra format, refs #25745
• src/hg/utils/automation/doRepeatMasker.pl
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    de697f3424320f0679649fcba305e3b8641d3cad Fri Jun 19 12:19:07 2020 -0700
    attempt to work without an NCBI lift file and issue warning refs #23367
• src/hg/utils/faToVcf/faToVcf.c
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    aa03a541ef25d83f1542202f784c53500c434c2d Sat Jun 20 14:35:04 2020 -0700
    New util faToVcf for extracting single-nucleotide variants from multi-sequence FASTA alignment.
• src/hg/utils/faToVcf/makefile
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    aa03a541ef25d83f1542202f784c53500c434c2d Sat Jun 20 14:35:04 2020 -0700
    New util faToVcf for extracting single-nucleotide variants from multi-sequence FASTA alignment.
• src/hg/utils/otto/clinGen/checkClinGen.sh
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    37befdf6676de0022c60966291e21e5977dba086 Fri Jun 19 13:46:31 2020 -0700
    Adding clingen cnv and dosage otto job to source tree now that it's been running for a while, refs #25562
• src/hg/utils/otto/clinGen/clinGenWrapper.sh
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    37befdf6676de0022c60966291e21e5977dba086 Fri Jun 19 13:46:31 2020 -0700
    Adding clingen cnv and dosage otto job to source tree now that it's been running for a while, refs #25562
• src/hg/utils/otto/clinGen/makeCnv.sh
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    37befdf6676de0022c60966291e21e5977dba086 Fri Jun 19 13:46:31 2020 -0700
    Adding clingen cnv and dosage otto job to source tree now that it's been running for a while, refs #25562
• src/hg/utils/otto/clinGen/makeDosage.sh
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    37befdf6676de0022c60966291e21e5977dba086 Fri Jun 19 13:46:31 2020 -0700
    Adding clingen cnv and dosage otto job to source tree now that it's been running for a while, refs #25562
• src/hg/utils/otto/clinGen/processClinGenCnv.py
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    37befdf6676de0022c60966291e21e5977dba086 Fri Jun 19 13:46:31 2020 -0700
    Adding clingen cnv and dosage otto job to source tree now that it's been running for a while, refs #25562
• src/hg/utils/otto/clinGen/processClinGenDosage.py
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    37befdf6676de0022c60966291e21e5977dba086 Fri Jun 19 13:46:31 2020 -0700
    Adding clingen cnv and dosage otto job to source tree now that it's been running for a while, refs #25562
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    1af2fddea7e6ede49cc2b334a6c8e78df998c9fa Mon Jun 8 16:15:28 2020 -0700
    Nextstrain changed to a new set of clade definitions, but they still keep the old clade assignments around in a different tag. Make subtracks for both old and new sets of clades. refs #25188
• src/hg/utils/otto/nextstrainNcov/lineageColors.py
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    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
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    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/newick.py
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    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
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    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    1af2fddea7e6ede49cc2b334a6c8e78df998c9fa Mon Jun 8 16:15:28 2020 -0700
    Nextstrain changed to a new set of clade definitions, but they still keep the old clade assignments around in a different tag. Make subtracks for both old and new sets of clades. refs #25188
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    a113d7fcbb275fcfda2b51c2bc359900531a8c0d Tue Jun 9 13:26:57 2020 -0700
    Adding more tolerance for missing data in ncov.json so I can run on a dev build of Nextstrain.
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    abf5dba0ce1f1cf2d3f15624272bde0854aec681 Sat Jun 20 14:24:44 2020 -0700
    Don't ignore the 'mutations' that are changes between [ACGT] and '-' (missing info), because they can occasionally happen in the path of a nucleotide change, for example T28144- to -T28144C. fixes #25751
• src/hg/utils/otto/nextstrainNcov/nextstrainVcf.py
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    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
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    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/sampleCladeLineage.py
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    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
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    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/sampleLineage.py
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    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
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    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeBranchWithSamples.py
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    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeColorByLineage.py
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    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeIntersectNextstrain.py
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    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
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    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeIntersectVcf.py
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    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeLineage.py
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    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
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    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treePruneToSamples.py
  • lines changed 39, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/utils.py
  • lines changed 16, context: html, text, full: html, text
    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/vcf.py
  • lines changed 85, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/vcfPruneToSamples.py
  • lines changed 38, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/virusNames.py
  • lines changed 6, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/inc/genoFind.h
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    9aa8cb048fd8b72bb544b78d335dee347e8c207f Wed Jun 17 15:29:29 2020 -0700
    Increment blat version number. Now we konw if blat version is 36x7 or newer, the compiler optimization bug should be fixed. refs #25700
• src/inc/iupac.h
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    aa03a541ef25d83f1542202f784c53500c434c2d Sat Jun 20 14:35:04 2020 -0700
    New util faToVcf for extracting single-nucleotide variants from multi-sequence FASTA alignment.
• src/inc/srcVersion.h
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    e24be750c2eaaeb78ed10b81b44471b19476c6c1 Mon Jun 22 09:58:57 2020 -0700
    New version number v400
• src/lib/vcf.c
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    8d9367da0e57755641dbbf6498093f7e44f14f12 Sat Jun 20 13:27:08 2020 -0700
    VCF: support up to 64k genotypes, including haplotype+tree display. sorta refs #25278 The VCF parser currently has a hardcoded upper limit on the number of genotype columns. I increased that from 16k to 64k to support Rob Lanfear's SARS-CoV-2 tree w/40k nodes. It will keep growing, so I will probably want to revisit so that we allocate the array size needed instead of a hardcoded huge size when most VCF tracks don't have anywhere near that many. In vcfTracks.c, using 'unsigned short' for the gtHapOrder array limits the number of samples to 32k because the index into gtHapOrder is gtIx<<1+hapIx. Changed all the shorts to ints because we now have VCF with more than 32k genotype columns.
• src/utils/qa/weeklybld/buildEnv.csh
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    ba9760c85ff89f15590a5c5f26d6e08f40b46636 Mon Jun 22 09:51:48 2020 -0700
    v400 final build

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• files changed: 260