angie: changes by file

review to branch (2010-02-10 to 2010-02-16) v225

• src/hg/blastToPsl/makefile
  • 1.30 lines changed: 1, context: html, text, full: html, text
    kent/src/lib is 2, not 3 directory levels above.
• src/hg/hgGetAnn/hgGetAnn.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Added cgiSpoof so the new cgiOptionalString in hgFind.c doesn't make cgiInit freak out.
• src/hg/hgTracks/bamTrack.c
  • 1.25 lines changed: 5, context: html, text, full: html, text
    Fix: handle soft-clipping when fetching query sequence.
• src/hg/hgc/bamClick.c
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Added printTrackUiLink in doBamDetails.
  • 1.15 lines changed: 8, context: html, text, full: html, text
    Fix: handle soft-clipping when fetching query sequence.
• src/hg/hgc/hgc.h
  • 1.49 lines changed: 3, context: html, text, full: html, text
    Added printTrackUiLink in doBamDetails.
• src/hg/inc/bamFile.h
  • 1.14 lines changed: 6, context: html, text, full: html, text
    Fix: handle soft-clipping when fetching query sequence.
• src/hg/instinct/hgMicroscope/microscope/testMicroscopeSearch.o
  • 1.2 lines changed: 0, context: html, text, full: html, text
    .o files should not be checked in.
• src/hg/instinct/hgMicroscope/microscopeLoad/exampleLoadingScript/vgLoadTest.o
  • 1.2 lines changed: 0, context: html, text, full: html, text
    .o files should not be checked in.
• src/hg/lib/bamFile.c
  • 1.19 lines changed: 38, context: html, text, full: html, text
    Fix: handle soft-clipping when fetching query sequence.
• src/hg/lib/hgFind.c
  • 1.225 lines changed: 4, context: html, text, full: html, text
    In searchKnownCanonical, no need to include knownGene in the query because kgXref and knownCanonical can be joined directly - thanks for catching that Tim.
• src/hg/visiGene/microscope.as
  • 1.2 lines changed: 60, context: html, text, full: html, text
    Removing - Chris says they are not needed here.
• src/hg/visiGene/microscope.sql
  • 1.2 lines changed: 88, context: html, text, full: html, text
    Removing - Chris says they are not needed here.