File Changes for angie

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

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 9, context: html, text, full: html, text
    Code Review #8673 - thanks Tim!
• src/hg/hgTracks/vcfTrack.c
  • lines changed 39, 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.
    
  • lines changed 15, context: html, text, full: html, text
    Fix to haplotype clustering in VCF display: was still giving too much weight to missing data.
• src/hg/hgc/hgc.c
  • lines changed 29, 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."
    
  • lines changed 2, context: html, text, full: html, text
    Code Review #8673 - thanks Tim!
• src/hg/hgc/vcfClick.c
  • lines changed 27, 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/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 3, context: html, text, full: html, text
    Doc #5088 (clean up trackDb/README): fixing a couple bugs in 272ef2ef59 found by Tim.
• src/hg/lib/snp125Ui.c
  • lines changed 1, 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/makeDb/doc/hg18.txt
  • lines changed 4, context: html, text, full: html, text
    Track #1656 (GWAS catalog): bi-monthly update.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    Track #1656 (GWAS catalog): bi-monthly update.
  • lines changed 18, 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/makeDb/trackDb/chimp/panTro1/snp125.html
  • lines changed 52, 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/cow/bosTau3/snp127.html
  • lines changed 52, 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/dog/canFam1/snp125.html
  • lines changed 52, 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/human/hg19/snp130.html
  • lines changed 54, 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/human/hg19/snp137.shared.html
  • lines changed 9, 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.
    
  • lines changed 14, 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/trackDb.ra
  • lines changed 2, 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/makeDb/trackDb/human/snp131Clinical.html
  • lines changed 261, 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/human/snp131NonClinical.html
  • lines changed 265, 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/rat/rn4/snp125.html
  • lines changed 52, 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/snp125.html
  • lines changed 52, 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/snp126.html
  • lines changed 52, 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/snp127.html
  • lines changed 52, 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/snp128.html
  • lines changed 64, 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/snp129.html
  • lines changed 57, 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/snp130.html
  • lines changed 54, 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/snp131.html
  • lines changed 57, 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/snp132.shared.html
  • lines changed 57, 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/snp134.html
  • lines changed 36, 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/snp134.shared.html
  • lines changed 360, 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/snp134Common.html
  • lines changed 28, 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/snp134Flagged.html
  • lines changed 29, 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/snp134Mult.html
  • lines changed 25, 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/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):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.