Commits for angie

v255_base to v256_preview (2011-08-08 to 2011-08-16) v256

• Feature #2823 (VCF track handler): Added UI control over height of haplotype-sorting display.
  • src/hg/hgTracks/vcfTrack.c - lines changed 71, context: html, text, full: html, text
  • src/hg/inc/vcfUi.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/vcfUi.c - lines changed 25, context: html, text, full: html, text
• Feature #2823 (VCF track handler): Added summaries of genotype and allele freqs to details page.
  • src/hg/hgc/vcfClick.c - lines changed 39, context: html, text, full: html, text
• Feature #2821 (VCF parser): improved representation of alleles:parse ref and comma-sep'd alt allele string into count and array inside record, so callers don't all have to parse the comma-sep'd alternate allele string.
  • src/hg/hgTracks/vcfTrack.c - lines changed 34, context: html, text, full: html, text
  • src/hg/hgc/vcfClick.c - lines changed 53, context: html, text, full: html, text
  • src/hg/lib/pgSnp.c - lines changed 92, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 2, context: html, text, full: html, text
  • src/lib/tests/vcfParseTest.c - lines changed 1, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 22, context: html, text, full: html, text
• Feature #3710 (vcfTabix UI options): added checkbox to enable/disable haplotype sorting display.
  • src/hg/hgTracks/vcfTrack.c - lines changed 8, context: html, text, full: html, text
  • src/hg/inc/vcfUi.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/pgSnp.c - lines changed 18, context: html, text, full: html, text
  • src/hg/lib/vcfUi.c - lines changed 33, context: html, text, full: html, text
• Feature #3710 (vcfTabix UI options): added option to use pgSnp colors instead of blueRef/redAlt in haplotype sorting display.
  • src/hg/hgTracks/vcfTrack.c - lines changed 28, context: html, text, full: html, text
  • src/hg/inc/vcfUi.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/vcfUi.c - lines changed 37, context: html, text, full: html, text
• Feature #3711 (vcfTabix haplotype sorting display): Draw hierarchical tree in left label area (as much as can fit there).
  • src/hg/hgTracks/vcfTrack.c - lines changed 165, context: html, text, full: html, text
• Merge branch 'vcfDrawHapTree'
• Bug #454 (hgTables fills the error logs with no-content errors):Removing an old debugging printf that must have been accidentally committed.
  • src/hg/hgTables/hgTables.c - lines changed 2, context: html, text, full: html, text
• Feature #3711 (vcfTabix haplotype-sorting display): Limit the numberof variants close to the center variant that we use for clustering, to prevent the clustering from timing out in large regions with large genotype counts (e.g. 1094 genotypes from 1000 Genomes phase 1 interim).
  • src/hg/hgTracks/vcfTrack.c - lines changed 16, context: html, text, full: html, text
• MLQ #4908 (genomicSuperDups strand): genomicSuperDups' strand column isalready displayed in hgc output as "Other Position Relative Orientation" which is its real meaning (not the usual sense of the strand column). So don't tell bedPrintPos that we have bed 6, because then it prints out a confusing redundant "Strand:".
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text