angie: changes by commit

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

• Oops, backing out inadvertently added debugging track.
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra 1.51 - lines changed: 12, context: html, text, full: html, text
• Share bbiNameFromTable() between bedTrack.c and bigWigTrack.c.
  • src/hg/hgTracks/bedTrack.c 1.15 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/bigWigTrack.c 1.6 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.184 - lines changed: 3, 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.c 1.1574 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.85 - lines changed: 2, context: html, text, full: html, text
• Added support for samtools/libbam, disabled by default.
  • src/inc/common.mk 1.61 - lines changed: 11, context: html, text, full: html, text
• Adding rudimentary support for BAM (compressed alignments) files as a native track type.
  • src/hg/hgTracks/bamTrack.c 1.1 - lines changed: 156, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.185 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgTracks/makefile 1.84 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.86 - lines changed: 6, 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/human/hg18/trackDb.ra 1.399 - lines changed: 22, context: html, text, full: html, text
• Ahem, forgot to fix default visibility before checking in.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.400 - lines changed: 2, context: html, text, full: html, text
• bugfix: when using sf->qStart as mrnaS in drawCdsDiffBaseTickmarksOnly, correct for adjustment to target start.
  • src/hg/hgTracks/cds.c 1.101 - lines changed: 1, context: html, text, full: html, text
• Oops, reverse-complement BAM query sequence when on - strand.
  • src/hg/hgTracks/bamTrack.c 1.2 - lines changed: 2, context: html, text, full: html, text
• Added new baseColorUseSequence option lfExtra (use sequence in lf->extra).
  • src/hg/hgTracks/cds.c 1.102 - lines changed: 6, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.215 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/README 1.80 - lines changed: 1, 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.
  • src/hg/hgTracks/simpleTracks.c 1.87 - lines changed: 5, context: html, text, full: html, text
• Added baseColor settings to bamNA12878.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.401 - lines changed: 4, 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.
  • src/lib/htmshell.c 1.55 - lines changed: 5, context: html, text, full: html, text
• Updated MGI (jax%) tracks.
  • src/hg/makeDb/doc/mm9.txt 1.100 - lines changed: 16, context: html, text, full: html, text