Commits for angie

v271_preview2 to v271_base (2012-07-31 to 2012-08-07) v271

• Doc #5088 (clean up trackDb/README): fixing a couple bugs in 272ef2ef59 found by Tim.
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 3, context: html, text, full: html, text
• Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Adding splice_region_variant, defined by SO as "A sequence variant in
  which a change has occurred within the region of the splice site,
  either within 1-3 bases of the exon or 3-8 bases of the intron."
  
  • src/hg/hgc/hgc.c - lines changed 29, context: html, text, full: html, text
  • src/hg/lib/snp125Ui.c - lines changed 1, context: html, text, full: html, text
• Track #1656 (GWAS catalog): bi-monthly update.
  • src/hg/makeDb/doc/hg18.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 4, context: html, text, full: html, text
• Track #7964 (1000 Genomes Phase 1): added recently-released chrY.Fixed bugs with display of haploid genotype data.
  1000 Genomes' chrY has tons of missing calls, and it turns out that clustering
  results are much better if missing info is completely omitted from distance
  measure -- although the tree calls things identical that clearly aren't.
  
  • src/hg/hgTracks/vcfTrack.c - lines changed 39, context: html, text, full: html, text
  • src/hg/hgc/vcfClick.c - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
• Merge branch 'vcfY'
• Code Review #8673 - thanks Tim!
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text
• Fix to haplotype clustering in VCF display: was still giving too much weight to missing data.
  • src/hg/hgTracks/vcfTrack.c - lines changed 15, context: html, text, full: html, text
• Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
  so track details should make clear the relationship of dbSNP terms used in the table (and by
  dbSNP) to Sequence Ontology terms shown on the details page.
  I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
  never were released.
  
  • src/hg/makeDb/trackDb/chimp/panTro1/snp125.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau3/snp127.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam1/snp125.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/snp130.html - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/snp137.shared.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp131Clinical.html - lines changed 261, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp131NonClinical.html - lines changed 265, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/snp125.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp125.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp126.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp127.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp128.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp129.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp130.html - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp131.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp132.shared.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp134.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp134.shared.html - lines changed 360, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp134Common.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp134Flagged.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp134Mult.html - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp135.shared.html - lines changed 56, context: html, text, full: html, text
• Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):"internal term" --> "dbSNP term" as suggested by Brooke in note 12.
  
  • src/hg/makeDb/trackDb/human/hg19/snp137.shared.html - lines changed 14, context: html, text, full: html, text