angie: changes by file

branch to review (2009-10-27 to 2009-11-03) v219

• src/makefile
  • 1.69 lines changed: 1, context: html, text, full: html, text
    Hooking udcFuse into top-level build
• src/fuse/makefile
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Should have finished writing it first.
  • 1.1 lines changed: 13, context: html, text, full: html, text
    Hooking udcFuse into top-level build
• src/fuse/udcFuse/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    First cut, mostly works but performance is not yet satisfactory.
• src/fuse/udcFuse/udcFuse.c
  • 1.1 lines changed: 390, context: html, text, full: html, text
    First cut, mostly works but performance is not yet satisfactory.
• src/hg/hgCustom/hgCustom.c
  • 1.133 lines changed: 2, context: html, text, full: html, text
    Added setUdcCacheDir() as in hgTracks, hgc etc. Without it, files were being initialized in /tmp/udcCache not our locally configured /data/apache/trash/udcCache.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.506 lines changed: 8, context: html, text, full: html, text
    DGV: Change the default filter to include-all instead of exclude-none -- positive logic is more intuitive. (Thx b0b)
• src/hg/hgTracks/bamTrack.c
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Gordon Robertson request: make gray lighter for unpaired ends.
• src/hg/lib/bamFile.c
  • 1.12 lines changed: 71, context: html, text, full: html, text
    If udcFuse.mountPoint is set in hg.conf, translate BAM URLs into filenames underneath that mount point, which mirrors the local udc cacheDir's hierarchy. Open the URL for bam and the associated .bai index file using udc, to make sure that the translated filenames will exist.
• src/hg/lib/customFactory.c
  • 1.107 lines changed: 2, context: html, text, full: html, text
    Better error message in bamLoader.
• src/inc/udc.h
  • 1.11 lines changed: 19, context: html, text, full: html, text
    Support for udcFuse and apps that will read files from it: plug minor memory leaks, use errAbort not assert, make udcFileMayOpen public, make udcParseUrl public so apps can determine path to file in udcFuse, add udcPathToUrl and udcSizeFromCache so that udcFuse can report the correct total file size.
• src/lib/errCatch.c
  • 1.4 lines changed: 25, context: html, text, full: html, text
    Make errCatch POSIX thread (pthread) safe: instead of a single global stack, use per-thread stacks hashed by thread ID.
• src/lib/udc.c
  • 1.18 lines changed: 102, context: html, text, full: html, text
    Support for udcFuse and apps that will read files from it: plug minor memory leaks, use errAbort not assert, make udcFileMayOpen public, make udcParseUrl public so apps can determine path to file in udcFuse, add udcPathToUrl and udcSizeFromCache so that udcFuse can report the correct total file size.