angie: changes by commit

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

• 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/hgc/hgc.c 1.1514 - lines changed: 25, context: html, text, full: html, text
• Adding hapmapPhase setting to hapmapSnps. Adding hapmapRecombRate track.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.379 - lines changed: 16, 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/hgTrackUi/hgTrackUi.c 1.475 - lines changed: 22, context: html, text, full: html, text
  • src/hg/hgTracks/hapmapTrack.c 1.45 - lines changed: 440, context: html, text, full: html, text
  • src/hg/inc/hapmapSnps.h 1.7 - lines changed: 23, context: html, text, full: html, text
• Adding hapmapPhaseIIISummary: properties used to filter hapmapSnps in hgTracks.
  • src/hg/inc/hapmapPhaseIIISummary.h 1.1 - lines changed: 74, context: html, text, full: html, text
  • src/hg/lib/hapmapPhaseIIISummary.as 1.1 - lines changed: 24, context: html, text, full: html, text
  • src/hg/lib/hapmapPhaseIIISummary.c 1.1 - lines changed: 272, context: html, text, full: html, text
  • src/hg/lib/hapmapPhaseIIISummary.sql 1.1 - lines changed: 30, context: html, text, full: html, text
  • src/hg/lib/makefile 1.386 - lines changed: 1, 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/getOrthoSeq.pl 1.1 - lines changed: 57, 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/hapmapPhaseIIISummary.c 1.1 - lines changed: 253, context: html, text, full: html, text
  • src/hg/snp/snpLoad/makefile 1.46 - lines changed: 12, context: html, text, full: html, text
• More specific longLabel for hapmapSnps.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.380 - lines changed: 1, 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/hapmapSnps.html 1.34 - lines changed: 155, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/hapmapSnps.html 1.2 - lines changed: 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/hapmapSnps.html 1.1 - lines changed: 193, 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/doc/hg18.txt 1.353 - lines changed: 364, context: html, text, full: html, text
• HapMap SNPs heterozygosity label: tweaked to match hgTrackUi.
  • src/hg/hgc/hgc.c 1.1515 - lines changed: 2, 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.
  • src/hg/hgTracks/hapmapTrack.c 1.46 - 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/hgTrackUi/hgTrackUi.c 1.476 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgTracks/hapmapTrack.c 1.47 - lines changed: 12, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.68 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgc/hgc.c 1.1516 - lines changed: 10, 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.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.381 - lines changed: 58, 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/hapmapSnpsPhaseII.html 1.1 - lines changed: 178, context: html, text, full: html, text
• Added Human Genome Diversity Project tracks.
  • src/hg/makeDb/schema/all.joiner 1.699 - lines changed: 5, context: html, text, full: html, text