angie: changes by commit

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

• 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/hgConfig.c 1.22 - lines changed: 3, context: html, text, full: html, text
• Added refreshNamedSessionCustomTracks to DIRS.
  • src/hg/utils/makefile 1.16 - lines changed: 2, 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/customFactory.c 1.105 - lines changed: 68, 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/hgTracks/makefile 1.88 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgc/makefile 1.64 - lines changed: 3, context: html, text, full: html, text
  • src/inc/common.mk 1.71 - lines changed: 1, context: html, text, full: html, text
• Added support for bam as a custom track type.
  • src/hg/hgTracks/bamTrack.c 1.10 - lines changed: 9, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c 1.1601 - lines changed: 13, context: html, text, full: html, text
  • src/hg/hgc/bamClick.c 1.11 - lines changed: 11, context: html, text, full: html, text
  • src/hg/hgc/hgc.c 1.1578 - lines changed: 4, context: html, text, full: html, text
  • src/hg/inc/bamFile.h 1.11 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/bamFile.c 1.10 - lines changed: 17, context: html, text, full: html, text
  • src/hg/lib/customFactory.c 1.106 - lines changed: 41, context: html, text, full: html, text
• Support inclusion of other hg.conf files.
  • src/test/perllib/HgConf.pm 1.3 - lines changed: 38, context: html, text, full: html, text
• Added pgSjk to tablesIgnored (thx Brooke).
  • src/hg/makeDb/schema/all.joiner 1.740 - lines changed: 1, context: html, text, full: html, text
• Fixed INDEX.
  • src/hg/lib/pgSnp.sql 1.3 - lines changed: 1, context: html, text, full: html, text
• Updated link -- annoying when a working link disappears.
  • src/hg/makeDb/trackDb/human/hg18/pgSnp.html 1.9 - lines changed: 1, context: html, text, full: html, text