angie: changes by file

branch to review (2009-10-13 to 2009-10-20) v218

• src/hg/hgTrackUi/hgTrackUi.c
  • 1.505 lines changed: 2, context: html, text, full: html, text
    Implemented grayscale for base qualities and coloring by user-specified tag.
  • 1.504 lines changed: 60, context: html, text, full: html, text
    Added enhanced coloring options (user-requested) to hgTrackUi and implemented 3 out of 5 in hgTracks.
• src/hg/hgTracks/bamTrack.c
  • 1.12 lines changed: 136, context: html, text, full: html, text
    Implemented grayscale for base qualities and coloring by user-specified tag.
  • 1.11 lines changed: 177, context: html, text, full: html, text
    Added enhanced coloring options (user-requested) to hgTrackUi and implemented 3 out of 5 in hgTracks.
• src/hg/hgTracks/hgTracks.h
  • 1.187 lines changed: 11, context: html, text, full: html, text
    Added enhanced coloring options (user-requested) to hgTrackUi and implemented 3 out of 5 in hgTracks.
• src/hg/inc/bamFile.h
  • 1.12 lines changed: 5, context: html, text, full: html, text
    Implemented grayscale for base qualities and coloring by user-specified tag.
• src/hg/inc/hui.h
  • 1.140 lines changed: 23, context: html, text, full: html, text
    Added enhanced coloring options (user-requested) to hgTrackUi and implemented 3 out of 5 in hgTracks.
• src/hg/lib/bamFile.c
  • 1.11 lines changed: 50, context: html, text, full: html, text
    Implemented grayscale for base qualities and coloring by user-specified tag.
• src/hg/makeDb/trackDb/drosophila/dm1/flyreg.html
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Updated link to Dan Pollard's matrices and email (thx Brooke).
• src/hg/makeDb/trackDb/drosophila/dm2/flyreg2.html
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Updated link to Dan Pollard's matrices and email (thx Brooke).
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixing another broken link.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFilesInner.csh
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fixed syntax error in case of multiple previous logfiles.