Commits for angie

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

• Suppress "Variant Identifiers" option if this assembly has no snp table. (Thanks Jonathan!)fixes #13085
  
  • src/hg/hgVai/hgVai.c - lines changed 11, 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/hgc.c - lines changed 16, context: html, text, full: html, text
  • src/hg/hgc/vcfClick.c - lines changed 56, 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/hg/lib/pgSnp.c - lines changed 4, 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
  
  • src/lib/vcf.c - lines changed 24, 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/annoStreamVcf.c - lines changed 4, context: html, text, full: html, text