Commits for angie

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

• 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.
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 88, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra - lines changed 421, 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/dhcBamDenisova.html - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/dhcHumDerDenAnc.html - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/dhcVcfDenisovaPinky.html - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/dhcVcfModern.html - lines changed 7, context: html, text, full: html, text
• Use "L += ..." instead of "L = ..." to avoid losing inc/common.mk $USE_* tweaks.
  • src/utils/bbTest/makefile - 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/bigBed.c - lines changed 1, 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/hgTables/bigBed.c - lines changed 9, context: html, text, full: html, text
• Track #8886 (Denisova high-cov): Description & label corrections from Fernando Racimo.
  • src/hg/makeDb/trackDb/human/hg19/dhcHumDerDenAnc.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra - lines changed 56, 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 6, 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/tgpPhase1Accessibility.html - lines changed 119, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 22, 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/tgpPhase1.html - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 45, context: html, text, full: html, text
• Expose vcfFilePooledStr to callers (for example to share allele storage).
  • src/inc/vcf.h - lines changed 3, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 5, 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.
  
  • src/hg/hgTracks/vcfTrack.c - lines changed 36, 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/hgTracks.h - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/vcfTrack.c - lines changed 51, context: html, text, full: html, text
  • src/hg/hgc/vcfClick.c - lines changed 193, context: html, text, full: html, text
  • src/hg/lib/pgSnp.c - lines changed 7, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 9, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 37, 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/hgTracks/vcfTrack.c - lines changed 52, context: html, text, full: html, text