angie: changes by file

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

• src/hg/hgTrackUi/hgTrackUi.c
  • 1.513 lines changed: 10, 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.
  • 1.512 lines changed: 5, context: html, text, full: html, text
    Added BAM config help link (if file exists).
• src/hg/hgTracks/bamTrack.c
  • 1.23 lines changed: 6, context: html, text, full: html, text
    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/hgc/bamClick.c
  • 1.14 lines changed: 16, context: html, text, full: html, text
    Added read name (wasn't obvious!). Added overall position & size for paired reads.
• src/hg/hgc/hgc.c
  • 1.1585 lines changed: 5, 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/lib/bamFile.c
  • 1.18 lines changed: 15, 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/makeDb/doc/mm9.txt
  • 1.119 lines changed: 29, context: html, text, full: html, text
    IKMC (komp) update.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.579 lines changed: 1, context: html, text, full: html, text
    Resolved some strict regex warning from checkHgFindSpec -checkTermRegex mm9.
• src/hg/makeDb/trackDb/mouse/komp.html
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Corrections from Katrina.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.179 lines changed: 3, context: html, text, full: html, text
    Resolved some strict regex warning from checkHgFindSpec -checkTermRegex mm9.
  • 1.178 lines changed: 1, context: html, text, full: html, text
    Oops, copy-paste fix.
  • 1.177 lines changed: 9, 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/lib/rudp.c
  • 1.24 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/udc.c
  • 1.32 lines changed: 2, 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.