angie: changes by file

review to branch (2010-02-23 to 2010-03-02) v226

• src/getgene/makefile
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/hg/checkHgFindSpec/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/hg/checkTableCoords/makefile
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.515 lines changed: 5, context: html, text, full: html, text
    Added option to (not) display item names in bam tracks. Also, when coloring by alignment qual and not pairing, sort by score.
• src/hg/hgTracks/bamTrack.c
  • 1.27 lines changed: 30, context: html, text, full: html, text
    Added option to (not) display item names in bam tracks. Also, when coloring by alignment qual and not pairing, sort by score.
  • 1.26 lines changed: 10, context: html, text, full: html, text
    I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks.
• src/hg/inc/hui.h
  • 1.145 lines changed: 1, context: html, text, full: html, text
    Added option to (not) display item names in bam tracks. Also, when coloring by alignment qual and not pairing, sort by score.
• src/hg/inc/knetUdc.h
  • 1.1 lines changed: 10, context: html, text, full: html, text
    I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks.
• src/hg/lib/bamFile.c
  • 1.20 lines changed: 16, context: html, text, full: html, text
    If compiling with KNETFILE_HOOKS (samtools extension that lets us hook in udc for URL I/O), don't cd to trash while loading the index -- if udc.cacheDir is a relative path, then that breaks, and if using udc we don't need samtools' index-caching.
• src/hg/lib/knetUdc.c
  • 1.1 lines changed: 84, context: html, text, full: html, text
    I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks.
• src/hg/lib/makefile
  • 1.402 lines changed: 1, context: html, text, full: html, text
    I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks.
• src/hg/makeDb/doc/hg18.txt
  • 1.400 lines changed: 45, context: html, text, full: html, text
    gwasCatalog update
• src/hg/makeDb/doc/hg19.txt
  • 1.87 lines changed: 12, context: html, text, full: html, text
    gwasCatalog update
• src/hg/makeDb/trackDb/human/par.html
  • 1.2 lines changed: 3, context: html, text, full: html, text
    fixed a couple typos.
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.29 lines changed: 1, context: html, text, full: html, text
    Enforce capitalization of only the first word in commonName, to match dbDb convention.
• src/hg/visiGene/vgPrepImage/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/inc/common.mk
  • 1.76 lines changed: 5, context: html, text, full: html, text
    I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks.
• src/inc/portable.h
  • 1.29 lines changed: 3, context: html, text, full: html, text
    Added touchFile (like touch command).
• src/lib/osunix.c
  • 1.45 lines changed: 19, context: html, text, full: html, text
    Added touchFile (like touch command).
• src/lib/udc.c
  • 1.35 lines changed: 12, context: html, text, full: html, text
    No need to use sparseFile in addition to bitmap file for cache age/timeout, and it causes trouble when bitmap exists but sparseData doesn't (yet). Also, moved verbose() up to where it wouldn't cause segv.
  • 1.34 lines changed: 7, context: html, text, full: html, text
    Another tweak required to make the cache timeout work: when we do fetch info, update the cache file mod times to reset the cache timeout clock.
  • 1.33 lines changed: 9, context: html, text, full: html, text
    When getting updateTime and size from the cache bitmap file, get the real remote update time from the bitmap file contents, not the bitmap fileModTime.
• src/parasol/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/primeMate/makefile
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/wormAli/makefile
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).