angie: changes by file

review to branch (2009-03-03 to 2009-03-10) v202

• src/hg/hgTrackUi/hgTrackUi.c
  • 1.476 lines changed: 4, context: html, text, full: html, text
    Added support for hapmapSnpsPhaseII track (replaced by the new PhaseIII track in 18, but kept around in case folks relied on its het. calcs).
  • 1.475 lines changed: 22, context: html, text, full: html, text
    HapMap SNPs: Added distinction between expected and observed heterozygosity for filtering. Finally checking in Phase III filtering code in hgTracks/hapmapTrack.c.
• src/hg/hgTracks/hapmapTrack.c
  • 1.47 lines changed: 12, context: html, text, full: html, text
    Added support for hapmapSnpsPhaseII track (replaced by the new PhaseIII track in 18, but kept around in case folks relied on its het. calcs).
  • 1.46 lines changed: 1, context: html, text, full: html, text
    For filter 'matches minor human allele', make sure the minor allele has been observed in at least one sample.
  • 1.45 lines changed: 440, context: html, text, full: html, text
    HapMap SNPs: Added distinction between expected and observed heterozygosity for filtering. Finally checking in Phase III filtering code in hgTracks/hapmapTrack.c.
• src/hg/hgTracks/simpleTracks.c
  • 1.68 lines changed: 1, context: html, text, full: html, text
    Added support for hapmapSnpsPhaseII track (replaced by the new PhaseIII track in 18, but kept around in case folks relied on its het. calcs).
• src/hg/hgc/hgc.c
  • 1.1516 lines changed: 10, context: html, text, full: html, text
    Added support for hapmapSnpsPhaseII track (replaced by the new PhaseIII track in 18, but kept around in case folks relied on its het. calcs).
  • 1.1515 lines changed: 2, context: html, text, full: html, text
    HapMap SNPs heterozygosity label: tweaked to match hgTrackUi.
  • 1.1514 lines changed: 25, context: html, text, full: html, text
    HapMap SNPs: Added a trackDb setting to determine whether this particular track is Phase II or Phase III. Made the Heterozygosity labels more clear: the older versions of the track have expected het, but as of Phase III we're doing observed het. Fixed avg. obs. het calc ( oops, item- > score is minor allele freq not het! ) .
• src/hg/inc/hapmapPhaseIIISummary.h
  • 1.1 lines changed: 74, context: html, text, full: html, text
    Adding hapmapPhaseIIISummary: properties used to filter hapmapSnps in hgTracks.
• src/hg/inc/hapmapSnps.h
  • 1.7 lines changed: 23, context: html, text, full: html, text
    HapMap SNPs: Added distinction between expected and observed heterozygosity for filtering. Finally checking in Phase III filtering code in hgTracks/hapmapTrack.c.
• src/hg/lib/hapmapPhaseIIISummary.as
  • 1.1 lines changed: 24, context: html, text, full: html, text
    Adding hapmapPhaseIIISummary: properties used to filter hapmapSnps in hgTracks.
• src/hg/lib/hapmapPhaseIIISummary.c
  • 1.1 lines changed: 272, context: html, text, full: html, text
    Adding hapmapPhaseIIISummary: properties used to filter hapmapSnps in hgTracks.
• src/hg/lib/hapmapPhaseIIISummary.sql
  • 1.1 lines changed: 30, context: html, text, full: html, text
    Adding hapmapPhaseIIISummary: properties used to filter hapmapSnps in hgTracks.
• src/hg/lib/makefile
  • 1.386 lines changed: 1, context: html, text, full: html, text
    Adding hapmapPhaseIIISummary: properties used to filter hapmapSnps in hgTracks.
• src/hg/makeDb/doc/hg18.txt
  • 1.353 lines changed: 364, context: html, text, full: html, text
    Added HapMap Recomb Rate (rel22) and updated HapMap SNPs (rel27). Moved a shared inline script out (to hg/snp/snpLoad/getOrthoSeq.pl).
• src/hg/makeDb/schema/all.joiner
  • 1.699 lines changed: 5, context: html, text, full: html, text
    Added Human Genome Diversity Project tracks.
• src/hg/makeDb/trackDb/human/hapmapSnps.html
  • 1.34 lines changed: 155, context: html, text, full: html, text
    Moved human/hapmapSnps.html down to human/hg18/hapmapSnps.html. Added clarification of what is meant by heterozygosity in old and new HapMap SNPs.
• src/hg/makeDb/trackDb/human/hg17/hapmapSnps.html
  • 1.2 lines changed: 22, context: html, text, full: html, text
    Moved human/hapmapSnps.html down to human/hg18/hapmapSnps.html. Added clarification of what is meant by heterozygosity in old and new HapMap SNPs.
• src/hg/makeDb/trackDb/human/hg18/hapmapSnps.html
  • 1.1 lines changed: 193, context: html, text, full: html, text
    Moved human/hapmapSnps.html down to human/hg18/hapmapSnps.html. Added clarification of what is meant by heterozygosity in old and new HapMap SNPs.
• src/hg/makeDb/trackDb/human/hg18/hapmapSnpsPhaseII.html
  • 1.1 lines changed: 178, context: html, text, full: html, text
    Resurrecting old human/hapmapSnps.html as the renamed hapmapSnpsPhaseII. Added note about heterozygosity calculation and latest HapMap pub ref.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.381 lines changed: 58, context: html, text, full: html, text
    Added hapmapSnpsPhaseII track (replaced by the new PhaseIII track in hg18, but kept around in case folks relied on its het. calcs). Added hapmapPhase setting to snp129. Just for kicks, checking in hapmapRecombRateBW, a BigWig.
  • 1.380 lines changed: 1, context: html, text, full: html, text
    More specific longLabel for hapmapSnps.
  • 1.379 lines changed: 16, context: html, text, full: html, text
    Adding hapmapPhase setting to hapmapSnps. Adding hapmapRecombRate track.
• src/hg/snp/snpLoad/getOrthoSeq.pl
  • 1.1 lines changed: 57, context: html, text, full: html, text
    Adding script used by both snp129 and hapmapSnps orthologous allele tracks, to get the base value at the liftOver'd position in the other org.
• src/hg/snp/snpLoad/hapmapPhaseIIISummary.c
  • 1.1 lines changed: 253, context: html, text, full: html, text
    Adding hapmapPhaseIIISummary, which distills hapmapSnps* and hapmapAlleles* columns into a loading file for the hapmapPhaseIIISummary table, which is used to filter hapmapSnps subtracks in hgTracks.
• src/hg/snp/snpLoad/makefile
  • 1.46 lines changed: 12, context: html, text, full: html, text
    Adding hapmapPhaseIIISummary, which distills hapmapSnps* and hapmapAlleles* columns into a loading file for the hapmapPhaseIIISummary table, which is used to filter hapmapSnps subtracks in hgTracks.