angie: changes by file

review to branch (2009-10-06 to 2009-10-13) v217

• src/hg/hgTracks/bamTrack.c
  • 1.10 lines changed: 9, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/hgTracks/hgTracks.c
  • 1.1601 lines changed: 13, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/hgTracks/makefile
  • 1.88 lines changed: 3, context: html, text, full: html, text
    Use of samtools is spreading in the tree, so (if USE_BAM) add SAMLIB to L at the top level (inc/common.mk).
• src/hg/hgc/bamClick.c
  • 1.11 lines changed: 11, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/hgc/hgc.c
  • 1.1578 lines changed: 4, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/hgc/makefile
  • 1.64 lines changed: 3, context: html, text, full: html, text
    Use of samtools is spreading in the tree, so (if USE_BAM) add SAMLIB to L at the top level (inc/common.mk).
• src/hg/inc/bamFile.h
  • 1.11 lines changed: 3, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/lib/bamFile.c
  • 1.10 lines changed: 17, context: html, text, full: html, text
    Added support for bam as a custom track type.
• src/hg/lib/customFactory.c
  • 1.106 lines changed: 41, context: html, text, full: html, text
    Added support for bam as a custom track type.
  • 1.105 lines changed: 68, context: html, text, full: html, text
    A little code cleanup: removed vestigial save/restore of env vars, improved a couple warning messages, replaced dangerous use of stack variable outside its scope w/dyString, removed some unnecessary uses of dyString.
• src/hg/lib/hgConfig.c
  • 1.22 lines changed: 3, context: html, text, full: html, text
    Don't require user-read-only for included files (just ~/.hg.conf itself). This allows us to include our cgi-bin-\angie/hg.conf files, and simply override the db.user and password in ~/.hg.conf.
• src/hg/lib/pgSnp.sql
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixed INDEX.
• src/hg/makeDb/schema/all.joiner
  • 1.740 lines changed: 1, context: html, text, full: html, text
    Added pgSjk to tablesIgnored (thx Brooke).
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Updated link -- annoying when a working link disappears.
• src/hg/utils/makefile
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Added refreshNamedSessionCustomTracks to DIRS.
• src/inc/common.mk
  • 1.71 lines changed: 1, context: html, text, full: html, text
    Use of samtools is spreading in the tree, so (if USE_BAM) add SAMLIB to L at the top level (inc/common.mk).
• src/test/perllib/HgConf.pm
  • 1.3 lines changed: 38, context: html, text, full: html, text
    Support inclusion of other hg.conf files.