angie: changes by file

review to branch (2009-12-09 to 2009-12-14) v221

• src/hg/hgTrackUi/hgTrackUi.c
  • 1.510 lines changed: 5, context: html, text, full: html, text
    A couple other places where cds-reference needs to be omitted from the list of SNP functions if version >= 130 (Thanks again Katrina!). Also removed an extraneous comment left over from a branch tag move demo (1.429).
• src/hg/hgTracks/bamTrack.c
  • 1.19 lines changed: 13, context: html, text, full: html, text
    Got rid of bogus bamIgnoreStrand() -- make useStrand explicit. Added auto-detect of missing 'chr' in sequence names, so stripPrefix setting is no longer necessary. Better message for samopen failures.
• src/hg/hgc/bamClick.c
  • 1.13 lines changed: 24, context: html, text, full: html, text
    Got rid of bogus bamIgnoreStrand() -- make useStrand explicit. Added auto-detect of missing 'chr' in sequence names, so stripPrefix setting is no longer necessary. Better message for samopen failures.
• src/hg/inc/bamFile.h
  • 1.13 lines changed: 16, context: html, text, full: html, text
    Got rid of bogus bamIgnoreStrand() -- make useStrand explicit. Added auto-detect of missing 'chr' in sequence names, so stripPrefix setting is no longer necessary. Better message for samopen failures.
• src/hg/inc/hui.h
  • 1.144 lines changed: 4, context: html, text, full: html, text
    'Color by bases' labels: use 'mRNA bases' only when we have coding region info; otherwise, use 'item bases' because items are generally not mRNAs.
• src/hg/lib/bamFile.c
  • 1.17 lines changed: 52, context: html, text, full: html, text
    Got rid of bogus bamIgnoreStrand() -- make useStrand explicit. Added auto-detect of missing 'chr' in sequence names, so stripPrefix setting is no longer necessary. Better message for samopen failures.
• src/hg/lib/customTrack.c
  • 1.180 lines changed: 1, context: html, text, full: html, text
    Null check to prevent segv in command line runs (cgiScriptName returns NULL unless env var SCRIPT_NAME has been set).
• src/hg/lib/hui.c
  • 1.252 lines changed: 4, context: html, text, full: html, text
    'Color by bases' labels: use 'mRNA bases' only when we have coding region info; otherwise, use 'item bases' because items are generally not mRNAs.
• src/hg/makeDb/trackDb/human/hg19/snp130.html
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Removed mention of cds-reference since we no longer include that in the table (thx Katrina!).