angie: changes by commit

branch to review (2010-01-05 to 2010-01-12) v223

• Oops, don't use global var position -- when we zoom, that is not updated and still has the old pos. Use chromName:winStart-winEnd instead (samtools uses 0-based offsets).
  • src/hg/hgTracks/bamTrack.c 1.23 - lines changed: 6, context: html, text, full: html, text
• In debug message, cast pointer to 32-bit unsigned instead of 64-bit so it doesn't break the 32-bit build.
  • src/lib/udc.c 1.32 - lines changed: 2, context: html, text, full: html, text
• doHapMapSnpsAllPops: don't warn about differering alleles if one is the empty string -- in older hapmapSnps (phase II) tables, allele2 was empty when homoCount2 and heteroCount were both 0.
  • src/hg/hgc/hgc.c 1.1585 - lines changed: 5, context: html, text, full: html, text
• IKMC (komp) update.
  • src/hg/makeDb/doc/mm9.txt 1.119 - lines changed: 29, context: html, text, full: html, text
• Corrections from Katrina.
  • src/hg/makeDb/trackDb/mouse/komp.html 1.5 - lines changed: 5, context: html, text, full: html, text
• search spec for IKMC (komp): made regex a bit shorter, and inclusive of both old and new names. Added a prefix search so the items with new suffixes can still be found by gene name. Thanks to Katrina for finding that this was broken & fixing it for new names!
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.177 - lines changed: 9, context: html, text, full: html, text
• Oops, copy-paste fix.
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.178 - lines changed: 1, context: html, text, full: html, text
• Fixed comparison edge condition (not a huge problem, it just set tv_{sec,usec} to {0,1000000} not {1,0}). Thx Galt for pointing out that the net.c code was dupl'd from this.
  • src/lib/rudp.c 1.24 - lines changed: 1, context: html, text, full: html, text
• Resolved some strict regex warning from checkHgFindSpec -checkTermRegex mm9.
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.179 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.579 - lines changed: 1, context: html, text, full: html, text
• Added BAM config help link (if file exists).
  • src/hg/hgTrackUi/hgTrackUi.c 1.512 - lines changed: 5, context: html, text, full: html, text
• Changed some errAborts to warns so BAM track connection troubles don't prevent display of other tracks.
  • src/hg/lib/bamFile.c 1.18 - lines changed: 15, context: html, text, full: html, text
• Added read name (wasn't obvious!). Added overall position & size for paired reads.
  • src/hg/hgc/bamClick.c 1.14 - lines changed: 16, context: html, text, full: html, text
• In bamUi, add baseColor defaults to tdb if this is a custom track, as we do in hgTracks.c. Otherwise baseColor drop-down doesn't appear for BAM custom tracks.
  • src/hg/hgTrackUi/hgTrackUi.c 1.513 - lines changed: 10, context: html, text, full: html, text