angie: changes by file

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

• src/fuse/fuse.mk
  • 1.1 lines changed: 6, 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/makefile
  • 1.3 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/udcFuse/makefile
  • 1.3 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/hg/hgSession/hgSession.c
  • 1.53 lines changed: 1, context: html, text, full: html, text
    Oops, forgot a cloneString back in Oct. '08 (thx Pauline).
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.516 lines changed: 2, context: html, text, full: html, text
    Code review: ClosestToHome no longer necessary, and format string was hard to read. (thx Jim)
• src/hg/hgTracks/bamTrack.c
  • 1.30 lines changed: 13, context: html, text, full: html, text
    When item labels are suppressed, we still need to draw the leftLabel in dense mode (shortLabel).
  • 1.29 lines changed: 5, 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.
  • 1.28 lines changed: 83, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/hgTracks/cds.c
  • 1.105 lines changed: 1, context: html, text, full: html, text
    Fix for baseColorDrawItem being called w/drawOpt=off.
• src/hg/hgTracks/hgTracks.c
  • 1.1632 lines changed: 3, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/hgc/bamClick.c
  • 1.19 lines changed: 5, 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.
  • 1.18 lines changed: 12, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/hgc/bigBedClick.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Doh, there was a segv for rest==0x0 as in any bed3 bigBed.
• src/hg/inc/bamFile.h
  • 1.16 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.
  • 1.15 lines changed: 3, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/lib/bamFile.c
  • 1.22 lines changed: 3, 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.
  • 1.21 lines changed: 17, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/lib/customFactory.c
  • 1.118 lines changed: 11, context: html, text, full: html, text
    In bamLoader, report any warnings caught by errCatch even if there was no error.
• src/hg/lib/hdb.c
  • 1.419 lines changed: 8, context: html, text, full: html, text
    Fixed loadGrps to handle profiles.
• src/hg/lib/hui.c
  • 1.264 lines changed: 1, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/lib/knetUdc.c
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Use udcFileMayOpen and warn if it fails, rather than errAborting in udcFileOpen.
• src/hg/lib/snp125.as
  • 1.7 lines changed: 11, context: html, text, full: html, text
    Clarifications to comments after user question.
• src/inc/common.mk
  • 1.77 lines changed: 9, 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/https.h
  • 1.2 lines changed: 7, 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/net.h
  • 1.37 lines changed: 12, 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/lib/https.c
  • 1.5 lines changed: 9, 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/lib/internet.c
  • 1.11 lines changed: 1, 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/net.c
  • 1.79 lines changed: 138, 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/lib/udc.c
  • 1.36 lines changed: 12, 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.