angie: changes by file

branch to review (2009-06-23 to 2009-06-30) v209

• src/hg/hgTracks/bamTrack.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Oops, reverse-complement BAM query sequence when on - strand.
  • 1.1 lines changed: 156, context: html, text, full: html, text
    Adding rudimentary support for BAM (compressed alignments) files as a native track type.
• src/hg/hgTracks/bedTrack.c
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Share bbiNameFromTable() between bedTrack.c and bigWigTrack.c.
• src/hg/hgTracks/bigWigTrack.c
  • 1.6 lines changed: 6, context: html, text, full: html, text
    Share bbiNameFromTable() between bedTrack.c and bigWigTrack.c.
• src/hg/hgTracks/cds.c
  • 1.102 lines changed: 6, context: html, text, full: html, text
    Added new baseColorUseSequence option lfExtra (use sequence in lf->extra).
  • 1.101 lines changed: 1, context: html, text, full: html, text
    bugfix: when using sf->qStart as mrnaS in drawCdsDiffBaseTickmarksOnly, correct for adjustment to target start.
• src/hg/hgTracks/hgTracks.c
  • 1.1574 lines changed: 1, context: html, text, full: html, text
    Make a CGI parameter for measureTiming (not just hardcoded), for convenience and so we don't risk accidentally checking in measureTiming=TRUE.
• src/hg/hgTracks/hgTracks.h
  • 1.185 lines changed: 5, context: html, text, full: html, text
    Adding rudimentary support for BAM (compressed alignments) files as a native track type.
  • 1.184 lines changed: 3, context: html, text, full: html, text
    Share bbiNameFromTable() between bedTrack.c and bigWigTrack.c.
• src/hg/hgTracks/makefile
  • 1.84 lines changed: 4, context: html, text, full: html, text
    Adding rudimentary support for BAM (compressed alignments) files as a native track type.
• src/hg/hgTracks/simpleTracks.c
  • 1.87 lines changed: 5, context: html, text, full: html, text
    In linkedFeaturesDrawAt's hairy if() that decides whether to call baseColorDrawItem, !psl no longer cuts it as a test for whether we are drawing codons.
  • 1.86 lines changed: 6, context: html, text, full: html, text
    Adding rudimentary support for BAM (compressed alignments) files as a native track type.
  • 1.85 lines changed: 2, context: html, text, full: html, text
    Make a CGI parameter for measureTiming (not just hardcoded), for convenience and so we don't risk accidentally checking in measureTiming=TRUE.
• src/hg/lib/hui.c
  • 1.215 lines changed: 3, context: html, text, full: html, text
    Added new baseColorUseSequence option lfExtra (use sequence in lf->extra).
• src/hg/makeDb/doc/mm9.txt
  • 1.100 lines changed: 16, context: html, text, full: html, text
    Updated MGI (jax%) tracks.
• src/hg/makeDb/trackDb/README
  • 1.80 lines changed: 1, context: html, text, full: html, text
    Added new baseColorUseSequence option lfExtra (use sequence in lf->extra).
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.401 lines changed: 4, context: html, text, full: html, text
    Added baseColor settings to bamNA12878.
  • 1.400 lines changed: 2, context: html, text, full: html, text
    Ahem, forgot to fix default visibility before checking in.
  • 1.399 lines changed: 22, context: html, text, full: html, text
    Adding experimental tracks with a spot of 1000Genomes data for HapMap individual NA12878 on chr22.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.51 lines changed: 12, context: html, text, full: html, text
    Oops, backing out inadvertently added debugging track.
• src/inc/common.mk
  • 1.61 lines changed: 11, context: html, text, full: html, text
    Added support for samtools/libbam, disabled by default.
• src/lib/htmshell.c
  • 1.55 lines changed: 5, context: html, text, full: html, text
    Pass a file pointer to htmlWarnBoxSetup, so when we are creating trash/ html files for a frameset, the script is printed to the files not stdout.