Commits for angie

v258_preview2 to v258_base (2011-10-04 to 2011-10-10) v258

• Fixed an incorrect regex substr index for VCF FILTER or ALT header defs.
  • src/lib/vcf.c - lines changed 2, context: html, text, full: html, text
• Feature #3710 (vcfTabix UI options): added filtering by value of FILTER column.
  • src/hg/hgTracks/vcfTrack.c - lines changed 31, context: html, text, full: html, text
  • src/hg/lib/vcfUi.c - lines changed 44, context: html, text, full: html, text
• Added description of optional filtering by FILTER column values.
  • src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html - lines changed 5, context: html, text, full: html, text
• Loosened regex and handle new non-numeric values of ##FORMAT's "Number"introduced in VCF 4.1.
  • src/lib/vcf.c - lines changed 9, context: html, text, full: html, text
• Filter VCF items at load time so they apply to haplotype sorting mode too (oops).
  • src/hg/hgTracks/vcfTrack.c - lines changed 24, context: html, text, full: html, text
• Feature #3710 (vcfTabix UI options): added optional filter on min QUAL score.
  • src/hg/hgTracks/vcfTrack.c - lines changed 37, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html - lines changed 6, context: html, text, full: html, text
  • src/hg/inc/vcfUi.h - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/vcfUi.c - lines changed 24, context: html, text, full: html, text