angie: changes by commit

branch to review (2010-03-02 to 2010-03-16) v227

• Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
  • src/hg/hgTracks/bamTrack.c 1.28 - lines changed: 83, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c 1.1632 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgc/bamClick.c 1.18 - lines changed: 12, context: html, text, full: html, text
  • src/hg/inc/bamFile.h 1.15 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/bamFile.c 1.21 - lines changed: 17, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.264 - lines changed: 1, context: html, text, full: html, text
• Fix for baseColorDrawItem being called w/drawOpt=off.
  • src/hg/hgTracks/cds.c 1.105 - lines changed: 1, context: html, text, full: html, text
• Pass sql conn into bamFileNameFromTable, so we can get it from hAllocConnTrack, to support use of hg.conf profiles.
  • src/hg/hgTracks/bamTrack.c 1.29 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgc/bamClick.c 1.19 - lines changed: 5, context: html, text, full: html, text
  • src/hg/inc/bamFile.h 1.16 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/bamFile.c 1.22 - lines changed: 3, context: html, text, full: html, text
• Fixed loadGrps to handle profiles.
  • src/hg/lib/hdb.c 1.419 - lines changed: 8, context: html, text, full: html, text
• Oops, forgot a cloneString back in Oct. '08 (thx Pauline).
  • src/hg/hgSession/hgSession.c 1.53 - lines changed: 1, context: html, text, full: html, text
• Clarifications to comments after user question.
  • src/hg/lib/snp125.as 1.7 - lines changed: 11, context: html, text, full: html, text
• Code review: ClosestToHome no longer necessary, and format string was hard to read. (thx Jim)
  • src/hg/hgTrackUi/hgTrackUi.c 1.516 - lines changed: 2, context: html, text, full: html, text
• Doh, there was a segv for rest==0x0 as in any bed3 bigBed.
  • src/hg/hgc/bigBedClick.c 1.10 - lines changed: 1, context: html, text, full: html, text
• Moving the USE_FUSE addition of L += -lfuse to just this directory, so execs created in the rest of the tree don't crash on machines that don't have libfuse.
  • src/fuse/fuse.mk 1.1 - lines changed: 6, context: html, text, full: html, text
  • src/fuse/makefile 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/fuse/udcFuse/makefile 1.3 - lines changed: 1, context: html, text, full: html, text
• Moving the USE_FUSE addition of L += -lfuse to src/fuse only, so execs created in the rest of the tree don't crash on machines that don't have libfuse.
  • src/inc/common.mk 1.77 - lines changed: 9, context: html, text, full: html, text
• When item labels are suppressed, we still need to draw the leftLabel in dense mode (shortLabel).
  • src/hg/hgTracks/bamTrack.c 1.30 - lines changed: 13, context: html, text, full: html, text
• Instead of errAborting in low-level net.c routines, pass errors up to higher-level code, most of which already checks for error return values.
  • src/inc/https.h 1.2 - lines changed: 7, context: html, text, full: html, text
  • src/inc/net.h 1.37 - lines changed: 12, context: html, text, full: html, text
  • src/lib/https.c 1.5 - lines changed: 9, context: html, text, full: html, text
  • src/lib/net.c 1.79 - lines changed: 138, context: html, text, full: html, text
  • src/lib/udc.c 1.36 - lines changed: 12, context: html, text, full: html, text
• Use udcFileMayOpen and warn if it fails, rather than errAborting in udcFileOpen.
  • src/hg/lib/knetUdc.c 1.3 - lines changed: 6, context: html, text, full: html, text
• Taking untranslated h_errno out of warning message -- IMO it adds confusion instead of clarification when 99.99999% of the time, the problem is a typo in host name. man h_errno says that herror and hstrerror are obsolete, bummer.
  • src/lib/internet.c 1.11 - lines changed: 1, context: html, text, full: html, text
• In bamLoader, report any warnings caught by errCatch even if there was no error.
  • src/hg/lib/customFactory.c 1.118 - lines changed: 11, context: html, text, full: html, text