File Changes for angie

v364_preview2 to v364_base (2018-04-09 to 2018-04-16) v364

• src/hg/hgTables/vcf.c
  • lines changed 2, context: html, text, full: html, text
    3d834d96bf126177048d391f68a082969a98e243 Mon Apr 9 16:01:03 2018 -0700
    vcfTabOut was missing explainWhyNoResults. Thanks BrianL! refs #21218
• src/hg/hgVai/hgVai.c
  • lines changed 3, context: html, text, full: html, text
    17230d72f860c8003411033dad26d9433a65a744 Tue Apr 10 09:04:29 2018 -0700
    Clarify what 'official GENCODE release' means (as opposed to knownGene GENCODE-but-not-really). Thx BrianL refs #21142
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    5b4fcca505f362e2fd288f57d8d8dd2de1148d6c Wed Apr 11 11:47:25 2018 -0700
    Make POST the formMethod default instead of GET, to support long lists of rsIds / HGVS terms. Let the user know that unlike the position/search input that accepts HGVS-ish terms with gene symbols, hgVai needs specific transcript IDs. Thanks Jairo! refs #21142
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    d7e9c64795289915beea9e389a0218bddd111ba0 Wed Apr 11 12:07:14 2018 -0700
    oops, I omitted part of the regex in 5b4fcca50!
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    193eba89efc0c2cb8e61e58f75855cff4cae408b Wed Apr 11 17:44:38 2018 -0700
    Filter symbolic alleles out of dbSNP observed alleles and warn user. Make warnings reappear on subsequent queries even when we don't rebuild the VCF file by saving the warnings in a file too. variantProjector doesn't accept symbolic alleles, and dbSNP has all kinds of cruft in its observed alleles. One kind that occurs frequently is "lengthTooLong" -- sometimes in that case the alleles can be recovered from the allele frequency columns. Also ignore lines starting with "#" in rsId input using lineFileNextReal . refs #21142 note-24 -- thanks Jairo for finding the 'lengthTooLong' problem!
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
  • lines changed 7, context: html, text, full: html, text
    77bfb6f5861adb7663082ac74813cbb264cb43fc Tue Apr 10 14:02:15 2018 -0700
    Adding description of no_sequence_alteration to hgVai help, thanks Jairo! refs #21204
• src/hg/lib/annoGratorGpVar.c
  • lines changed 2, context: html, text, full: html, text
    ae875f4d5874c2dec0e6c584a59681e8beed7b64 Wed Apr 11 14:17:58 2018 -0700
    Yikes, was storing an unallocated var from the stack in a hash. Now it's allocated. Thanks Jairo! refs #21142 note-25
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    4672870e2141c49dc20bf1346f4bac0e0447f6dc Thu Apr 12 14:17:00 2018 -0700
    adding grcHhh38 (test db for adding patch sequences) to genbank build
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 26, context: html, text, full: html, text
    4672870e2141c49dc20bf1346f4bac0e0447f6dc Thu Apr 12 14:17:00 2018 -0700
    adding grcHhh38 (test db for adding patch sequences) to genbank build
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    4672870e2141c49dc20bf1346f4bac0e0447f6dc Thu Apr 12 14:17:00 2018 -0700
    adding grcHhh38 (test db for adding patch sequences) to genbank build