File Changes for angie

v299_preview to v299_preview2 (2014-04-14 to 2014-04-21) v299

• src/hg/hgVai/hgVai.c
  • lines changed 11, context: html, text, full: html, text
    Suppress "Variant Identifiers" option if this assembly has no snp table. (Thanks Jonathan!)fixes #13085
    
• src/hg/hgc/hgc.c
  • lines changed 16, context: html, text, full: html, text
    Matt and Tim noticed that the ESP6500 VCF track details had twoprintCustomTrackUrl invocations. One was in genericClickHandlerPlus
    and it used an incorrect name (known issue with using pgSnp display
    code for VCF). The second was inside doVcfTabixDetails, using
    the correct name. I moved doVcfTabixDetails and doVcfDetails out
    of genericClickHandlerPlus; now doMiddle calls them, and they call
    genericHeader and printTrackHtml in a shared function.
    refs #9329
    
• src/hg/hgc/vcfClick.c
  • lines changed 56, context: html, text, full: html, text
    Matt and Tim noticed that the ESP6500 VCF track details had twoprintCustomTrackUrl invocations. One was in genericClickHandlerPlus
    and it used an incorrect name (known issue with using pgSnp display
    code for VCF). The second was inside doVcfTabixDetails, using
    the correct name. I moved doVcfTabixDetails and doVcfDetails out
    of genericClickHandlerPlus; now doMiddle calls them, and they call
    genericHeader and printTrackHtml in a shared function.
    refs #9329
    
• src/hg/lib/pgSnp.c
  • lines changed 4, context: html, text, full: html, text
    When an insertion falls at the end of CDS, fetchCodons looks aheadto the next exon. However, when this happens in the last exon,
    there is no next exon so gene->chromStarts[i+1] is past the end
    of the array. Fix: make sure i+1 is a valid index before looking
    at the next exon.
    fixes #13089
    
• src/lib/annoStreamVcf.c
  • lines changed 4, context: html, text, full: html, text
    There was one more place where I needed to prepend "chr" to a VCFsequence name when comparing to region chrom.
    fixes #13093
    
• src/lib/vcf.c
  • lines changed 24, context: html, text, full: html, text
    vcfNextRecord was using lineFileChop instead of lineFileChopTab,which masked a data bug in 1000 Genomes Phase 1 VCF: some lines have
    an extra tab character at the end. Now we chop by tabs, but ignore
    a single empty extra column because an extra tab at the end is a
    pretty common error.
    fixes #13091