File Changes for angie

v293_preview to v293_preview2 (2013-11-18 to 2013-12-02) v293

• src/hg/hgTables/mainPage.c
  • lines changed 3, context: html, text, full: html, text
    Adding the option for hyperlinks output in a couple places whereit was missing, for bedGraph and microarray tracks.
    Hyperlinks output also works for database wiggle tracks, but not
    for bigWig. refs #12198
    
• src/hg/hgVai/hgVai.c
  • lines changed 40, context: html, text, full: html, text
    Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
    Made improvements to the display of symbolic alleles from dbSNP.
    Fixed strand bug in parseDbSnpAltAlleles. Thanks Jonathan!
    refs #11460 (hgVai: paste/upload variant input options)
    
  • lines changed 4, context: html, text, full: html, text
    I misunderstood the SO term NMD_transcript_variant to mean 'a variantthat induces nonsense-mediate decay', i.e. worse than just a stop-gain.
    However, the term actually means 'variant in a transcript that is
    *already* subject to NMD', i.e. less serious than a variant in an
    intron of a gene that gets translated. gpFx.c now has different
    logic for assigning that term, and hgVai has a new filtering option.
    fixes #12205
    
  • lines changed 6, context: html, text, full: html, text
    Include gene track in trash file name for hgVai's Artificial ExampleVariants, because example variants built with one gene track might
    not have any hits in another.
    
  • lines changed 2, context: html, text, full: html, text
    Fix segfault in databases with no snpNNN tables.
  • lines changed 2, context: html, text, full: html, text
    Updating reference for dbNSFP.
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
  • lines changed 7, context: html, text, full: html, text
    I misunderstood the SO term NMD_transcript_variant to mean 'a variantthat induces nonsense-mediate decay', i.e. worse than just a stop-gain.
    However, the term actually means 'variant in a transcript that is
    *already* subject to NMD', i.e. less serious than a variant in an
    intron of a gene that gets translated. gpFx.c now has different
    logic for assigning that term, and hgVai has a new filtering option.
    fixes #12205
    
• src/hg/inc/annoGratorGpVar.h
  • lines changed 1, context: html, text, full: html, text
    I misunderstood the SO term NMD_transcript_variant to mean 'a variantthat induces nonsense-mediate decay', i.e. worse than just a stop-gain.
    However, the term actually means 'variant in a transcript that is
    *already* subject to NMD', i.e. less serious than a variant in an
    intron of a gene that gets translated. gpFx.c now has different
    logic for assigning that term, and hgVai has a new filtering option.
    fixes #12205
    
• src/hg/lib/annoFormatVep.c
  • lines changed 1, context: html, text, full: html, text
    User request from Case: don't truncate alt allele column so readily.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 1, context: html, text, full: html, text
    Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
    Made improvements to the display of symbolic alleles from dbSNP.
    Fixed strand bug in parseDbSnpAltAlleles. Thanks Jonathan!
    refs #11460 (hgVai: paste/upload variant input options)
    
  • lines changed 3, context: html, text, full: html, text
    I misunderstood the SO term NMD_transcript_variant to mean 'a variantthat induces nonsense-mediate decay', i.e. worse than just a stop-gain.
    However, the term actually means 'variant in a transcript that is
    *already* subject to NMD', i.e. less serious than a variant in an
    intron of a gene that gets translated. gpFx.c now has different
    logic for assigning that term, and hgVai has a new filtering option.
    fixes #12205
    
• src/hg/lib/genePred.c
  • lines changed 2, context: html, text, full: html, text
    vintage 2005 bug -- genePredNmdTarget was practically guaranteed toreturn FALSE for genes on the - strand because it was comparing a
    relative coord to an absolute coord.
    
• src/hg/lib/gpFx.c
  • lines changed 3, context: html, text, full: html, text
    Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
    Made improvements to the display of symbolic alleles from dbSNP.
    Fixed strand bug in parseDbSnpAltAlleles. Thanks Jonathan!
    refs #11460 (hgVai: paste/upload variant input options)
    
  • lines changed 71, context: html, text, full: html, text
    I misunderstood the SO term NMD_transcript_variant to mean 'a variantthat induces nonsense-mediate decay', i.e. worse than just a stop-gain.
    However, the term actually means 'variant in a transcript that is
    *already* subject to NMD', i.e. less serious than a variant in an
    intron of a gene that gets translated. gpFx.c now has different
    logic for assigning that term, and hgVai has a new filtering option.
    fixes #12205
    
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 2, context: html, text, full: html, text
    Updating test file to match new understanding of NMD_transcript_variant(should have been part of 4c4eb6b4f0) refs #12205
    
• src/hg/lib/variant.c
  • lines changed 1, context: html, text, full: html, text
    Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
    Made improvements to the display of symbolic alleles from dbSNP.
    Fixed strand bug in parseDbSnpAltAlleles. Thanks Jonathan!
    refs #11460 (hgVai: paste/upload variant input options)
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    Oops, neglected to add a new identifier rule for lrgTranscriptAliand associated tables. Thanks Jonathan! refs #11863
    
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Removed duplicate entry for refreshNamedSessionCustomTracks (see ${buildRefresh}).
• src/lib/annoOption.c
  • lines changed 2, context: html, text, full: html, text
    Fixing ridiculous uninitialized use error found by Hiram and new Mac gcc.refs #12209
    
• src/lib/vcf.c
  • lines changed 82, context: html, text, full: html, text
    Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
    Made improvements to the display of symbolic alleles from dbSNP.
    Fixed strand bug in parseDbSnpAltAlleles. Thanks Jonathan!
    refs #11460 (hgVai: paste/upload variant input options)
    
  • lines changed 3, context: html, text, full: html, text
    Suppress a vcfFileErr about something that occurs in 1000 Genomes Phase 1VCF and is not really a big deal: if there's a keyword for which we're
    not expecting any particular number of values ("Number=." in header,
    def->fieldCount=-1), and the '=' is omitted when there are no values
    to report, just carry on and pretend we saw an '=' with no values
    after it.