angie: changes by file

review to branch (2009-07-27 to 2009-08-04) v212

• src/hg/hgTracks/bamTrack.c
  • 1.5 lines changed: 15, context: html, text, full: html, text
    Libified more commonly used BAM code from hgc and hgTracks.
• src/hg/hgc/bamClick.c
  • 1.2 lines changed: 44, context: html, text, full: html, text
    Libified more commonly used BAM code from hgc and hgTracks.
  • 1.1 lines changed: 137, context: html, text, full: html, text
    Added rudimentary click handler for bam tracks (Heng Li's alignment format).
• src/hg/hgc/hgc.c
  • 1.1563 lines changed: 4, context: html, text, full: html, text
    Added rudimentary click handler for bam tracks (Heng Li's alignment format).
• src/hg/hgc/hgc.h
  • 1.47 lines changed: 3, context: html, text, full: html, text
    Added rudimentary click handler for bam tracks (Heng Li's alignment format).
• src/hg/hgc/makefile
  • 1.62 lines changed: 4, context: html, text, full: html, text
    Added rudimentary click handler for bam tracks (Heng Li's alignment format).
• src/hg/inc/bamFile.h
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Oops, silly flag-testing bug (& comment clarification) in bamGetQuerySequence.
  • 1.2 lines changed: 28, context: html, text, full: html, text
    Libified more commonly used BAM code from hgc and hgTracks.
• src/hg/lib/bamFile.c
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Oops, silly flag-testing bug (& comment clarification) in bamGetQuerySequence.
  • 1.2 lines changed: 65, context: html, text, full: html, text
    Libified more commonly used BAM code from hgc and hgTracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.472 lines changed: 31, context: html, text, full: html, text
    Backing out previous change -- those tables are on hgwbeta after all, oops.
  • 1.471 lines changed: 31, context: html, text, full: html, text
    Workaround for appearance of extra column on hgwbeta which is missing some tables: add "release alpha" to the subtrack defs for hgwdev-only tables and the complete composite track def, and add a "release beta" composite track def which omits the subGroup item for the hgwdev-only tables.
• src/inc/common.mk
  • 1.66 lines changed: 4, context: html, text, full: html, text
    Fixed our local samtools installation so it's always in samtools/x86_64 (no exception for x86_64) -- thanks Mark.