angie: changes by commit

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

• Added rudimentary click handler for bam tracks (Heng Li's alignment format).
  • src/hg/hgc/bamClick.c 1.1 - lines changed: 137, context: html, text, full: html, text
  • src/hg/hgc/hgc.c 1.1563 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgc/hgc.h 1.47 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgc/makefile 1.62 - lines changed: 4, 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/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.471 - lines changed: 31, context: html, text, full: html, text
• Backing out previous change -- those tables are on hgwbeta after all, oops.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.472 - lines changed: 31, context: html, text, full: html, text
• Libified more commonly used BAM code from hgc and hgTracks.
  • src/hg/hgTracks/bamTrack.c 1.5 - lines changed: 15, context: html, text, full: html, text
  • src/hg/hgc/bamClick.c 1.2 - lines changed: 44, context: html, text, full: html, text
  • src/hg/inc/bamFile.h 1.2 - lines changed: 28, context: html, text, full: html, text
  • src/hg/lib/bamFile.c 1.2 - lines changed: 65, context: html, text, full: html, text
• Oops, silly flag-testing bug (& comment clarification) in bamGetQuerySequence.
  • src/hg/inc/bamFile.h 1.3 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/bamFile.c 1.3 - 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.
  • src/inc/common.mk 1.66 - lines changed: 4, context: html, text, full: html, text