File Changes for angie

v274_preview2 to v274_base (2012-10-02 to 2012-10-09) v274

• src/hg/hgTables/bigBed.c
  • lines changed 9, context: html, text, full: html, text
    If the .bb has no rows for the current chromosome, omit example row display.It would be nicer to just grab the first rows from the bigBed file in this case... don't have time today.
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
• src/hg/hgTracks/vcfTrack.c
  • lines changed 36, context: html, text, full: html, text
    VCF indel alleles always start with a reference base that is the same(e.g. for a dbSNP item with -/C, the VCF item starts with the reference
    base to the left like A/AC). Make the display consistent with dbSNP
    and other variation tracks by trimming the left neighboring base.
    
  • lines changed 51, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
  • lines changed 52, context: html, text, full: html, text
    Improved mouseover titles for VCF hap-cluster display: trim indel left base,abbreviate long alleles (e.g. 40kb deletion was causing giant mouseover titles
    to be ignored/truncated by web browser).
    
• src/hg/hgc/vcfClick.c
  • lines changed 193, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
• src/hg/lib/pgSnp.c
  • lines changed 7, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
• 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 88, context: html, text, full: html, text
    Track #8886 (Denisova high-coverage): Feedback from data providers:1. Separate "Fixed" subtracks into "Fixed" and "Fixed but in dbSNP".
    2. OK to combine SNCs and InDels to reduce # of subtracks.
    3. OK to hide non-CCDS gene changes, Synonymous, and Reg. Region by default.
    
  • lines changed 6, context: html, text, full: html, text
    Track #1656: GWAS Catalog bi-monthly update.
• src/hg/makeDb/trackDb/human/hg19/dhcBamDenisova.html
  • lines changed 7, context: html, text, full: html, text
    Track #8886 (Denisova High-Cov): added description for Human Derived,Denisova Ancestral; added link to SOM to other Denisova details pages,
    because unlike the article it isn't behind a paywall.
    
• src/hg/makeDb/trackDb/human/hg19/dhcHumDerDenAnc.html
  • lines changed 69, context: html, text, full: html, text
    Track #8886 (Denisova High-Cov): added description for Human Derived,Denisova Ancestral; added link to SOM to other Denisova details pages,
    because unlike the article it isn't behind a paywall.
    
  • lines changed 5, context: html, text, full: html, text
    Track #8886 (Denisova high-cov): Description & label corrections from Fernando Racimo.
• src/hg/makeDb/trackDb/human/hg19/dhcVcfDenisovaPinky.html
  • lines changed 7, context: html, text, full: html, text
    Track #8886 (Denisova High-Cov): added description for Human Derived,Denisova Ancestral; added link to SOM to other Denisova details pages,
    because unlike the article it isn't behind a paywall.
    
• src/hg/makeDb/trackDb/human/hg19/dhcVcfModern.html
  • lines changed 7, context: html, text, full: html, text
    Track #8886 (Denisova High-Cov): added description for Human Derived,Denisova Ancestral; added link to SOM to other Denisova details pages,
    because unlike the article it isn't behind a paywall.
    
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1.html
  • lines changed 80, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): draft description.Also label tweaks for 1000 Genomes accessible regions (#1079), and
    trackDb entries for Recombination Rates + Map composite track.
    
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1Accessibility.html
  • lines changed 119, context: html, text, full: html, text
    Track #1079 (1000 Genomes Phase 1 Accessible Regions):regions in which short reads map with sufficient mapping quality and enough
    (but not too much) depth to be trustworthy, by two sets of thresholds:
    pilot project and strict. Data & description from Tom Blackwell, UMich.
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra
  • lines changed 421, context: html, text, full: html, text
    Track #8886 (Denisova high-coverage): Feedback from data providers:1. Separate "Fixed" subtracks into "Fixed" and "Fixed but in dbSNP".
    2. OK to combine SNCs and InDels to reduce # of subtracks.
    3. OK to hide non-CCDS gene changes, Synonymous, and Reg. Region by default.
    
  • lines changed 56, context: html, text, full: html, text
    Track #8886 (Denisova high-cov): Description & label corrections from Fernando Racimo.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 22, context: html, text, full: html, text
    Track #1079 (1000 Genomes Phase 1 Accessible Regions):regions in which short reads map with sufficient mapping quality and enough
    (but not too much) depth to be trustworthy, by two sets of thresholds:
    pilot project and strict. Data & description from Tom Blackwell, UMich.
    
  • lines changed 7, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): draft description.Also label tweaks for 1000 Genomes accessible regions (#1079), and
    trackDb entries for Recombination Rates + Map composite track.
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 45, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): draft description.Also label tweaks for 1000 Genomes accessible regions (#1079), and
    trackDb entries for Recombination Rates + Map composite track.
    
• src/inc/vcf.h
  • lines changed 3, context: html, text, full: html, text
    Expose vcfFilePooledStr to callers (for example to share allele storage).
  • lines changed 9, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
• src/lib/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    Bug #9265 (bigBed with columns containing spaces is mangled in hgTables schema and output):chop by tabs, not spaces, in bigBedIntervalToRow. bedToBigBed always stores tab-sep.
    
• src/lib/vcf.c
  • lines changed 5, context: html, text, full: html, text
    Expose vcfFilePooledStr to callers (for example to share allele storage).
  • lines changed 37, context: html, text, full: html, text
    Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
    sharing w/hgc.
    2. Correct chromStart in hgTracks mapBox links to hgc when we have
    trimmed a left base.
    3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
    trimmed left base in parentheses for consistency with VCF file (and
    sometimes INFO fields that use left-inclusive coords/seqs).
    4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
    and hgc do their own abbreviating.
    
• src/utils/bbTest/makefile
  • lines changed 1, context: html, text, full: html, text
    Use "L += ..." instead of "L = ..." to avoid losing inc/common.mk $USE_* tweaks.