Commits for angie

v255_preview to v255_preview2 (2011-07-26 to 2011-08-02) v255

• Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements: made the Genotype Details table into a collapsible section; better display of QUAL and FILTER column values, which also involved improving the representation of those columns in src/inc/vcf.h.
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/vcfTrack.c - lines changed 29, context: html, text, full: html, text
  • src/hg/hgc/vcfClick.c - lines changed 52, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 6, context: html, text, full: html, text
  • src/hg/inc/trackDb.h - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/vcfUi.h - lines changed 18, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/vcfUi.c - lines changed 182, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 3, context: html, text, full: html, text
  • src/lib/linefile.c - lines changed 2, context: html, text, full: html, text
  • src/lib/tests/expected/vcfParse1kGNoGenotypes.out - lines changed 5, context: html, text, full: html, text
  • src/lib/tests/expected/vcfParse1kGWithGenotypes.out - lines changed 6, context: html, text, full: html, text
  • src/lib/tests/expected/vcfParseOldV3.out - lines changed 14, 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 21, context: html, text, full: html, text
• Track #4533 (High Seq Depth): loaded files into hg18 & hg19;initial trackDb & track description in place.
  • src/hg/makeDb/doc/hg18.txt - lines changed 74, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hiSeqDepth.html - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 41, context: html, text, full: html, text
• MLQ #4765: User translated BED6 to BAM, with '*' (placeholder) for the querysequence and quality scores, and our BAM display code didn't anticipate missing seq & base quals. Handle that case since it is legal BAM, albeit an unusual use of BAM. :)
  • src/hg/hgTracks/bamTrack.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgc/bamClick.c - lines changed 5, context: html, text, full: html, text
• Feature #2821 (VCF parser): correctly handle an INFO column that is just a"." placeholder.
  • src/lib/vcf.c - lines changed 9, context: html, text, full: html, text
• Feature #3711 (VCF haplotype sorting display): fixed goof in genotype summary mouseover text;corrected off-by-1 pixel outline that affected < base-level display.
  • src/hg/hgTracks/vcfTrack.c - lines changed 9, context: html, text, full: html, text
• Feature #2823 (VCF track handler): in hgc, let the user know when wecan't access the file (instead of just displaying nothing) and include custom url.
  • src/hg/hgc/vcfClick.c - lines changed 3, context: html, text, full: html, text
• Track #1656 (GWAS Catalog): bi-monthly update on hgwdev.
  • src/hg/makeDb/doc/hg18.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 3, context: html, text, full: html, text
• Track #1656 (GWAS Catalog): removing outdated release alpha,betaoverride for hg19.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 6, context: html, text, full: html, text