kent: changes by file

branch to review (2009-02-09 to 2009-02-17) v200

• src/blat/blat.c
  • 1.113 lines changed: 2, context: html, text, full: html, text
    Makin blat work with U's instead of T's if q=rna is set.
• src/blat/version.doc
  • 1.73 lines changed: 1, context: html, text, full: html, text
    Makin blat work with U's instead of T's if q=rna is set.
• src/hg/hgTracks/bedTrack.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Improving comment.
  • 1.2 lines changed: 17, context: html, text, full: html, text
    Creating bigBed type custom tracks.
• src/hg/hgTracks/hgTracks.c
  • 1.1553 lines changed: 19, context: html, text, full: html, text
    Creating bigBed type custom tracks.
• src/hg/hgc/bigBedClick.c
  • 1.2 lines changed: 36, context: html, text, full: html, text
    Creating bigBed type custom tracks.
• src/hg/hgc/hgc.c
  • 1.1505 lines changed: 2, context: html, text, full: html, text
    Creating bigBed type custom tracks.
  • 1.1504 lines changed: 2, context: html, text, full: html, text
    Making this handle clicks from bigWig custom tracks.
• src/hg/hgc/hgc.h
  • 1.45 lines changed: 3, context: html, text, full: html, text
    Creating bigBed type custom tracks.
  • 1.44 lines changed: 3, context: html, text, full: html, text
    Making this handle clicks from bigWig custom tracks.
• src/hg/hgc/wiggleClick.c
  • 1.31 lines changed: 25, context: html, text, full: html, text
    Making this handle clicks from bigWig custom tracks.
• src/hg/lib/customFactory.c
  • 1.96 lines changed: 34, context: html, text, full: html, text
    Creating bigBed type custom tracks.
• src/hg/makeDb/makefile
  • 1.40 lines changed: 1, context: html, text, full: html, text
    Adding hgBbiDbLink.
• src/hg/makeDb/doc/ucscGenes/hg18.ucscGenes11.csh
  • 1.17 lines changed: 13, context: html, text, full: html, text
    Updating worm link
• src/hg/makeDb/schema/dbSnoop/dbSnoop.c
  • 1.13 lines changed: 17, context: html, text, full: html, text
    Allowing remote databases.
• src/hg/near/hgNear/hgNear.c
  • 1.184 lines changed: 2, context: html, text, full: html, text
    Adding a comment.
• src/hg/oneShot/freen/freen.c
  • 1.86 lines changed: 27, context: html, text, full: html, text
    Testing simultanious writes.
  • 1.85 lines changed: 10, context: html, text, full: html, text
    Freen makes a 2 column file for testing.
• src/hg/oneShot/freen/test
  • 1.5 lines changed: 100000, context: html, text, full: html, text
    Removing stray (big!) test file that somehow got committed.
  • 1.4 lines changed: 100000, context: html, text, full: html, text
    Freen makes a 2 column file for testing.
• src/hg/utils/makefile
  • 1.12 lines changed: 2, context: html, text, full: html, text
    Adding crTree utilities.
• src/inc/bbiFile.h
  • 1.6 lines changed: 5, context: html, text, full: html, text
    Adding fieldCount and definedFieldCount to bbiFile header for bigBeds.
• src/inc/bigBed.h
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Adding fieldCount and definedFieldCount to bbiFile header for bigBeds.
• src/inc/genoFind.h
  • 1.80 lines changed: 1, context: html, text, full: html, text
    Makin blat work with U's instead of T's if q=rna is set.
• src/inc/sig.h
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Bumping bigBedSig due to slight change in format.
• src/jkOwnLib/splix.c
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Wrapping a read in netReadAll instead because it's so big it sometimes seems to come back in parts.
• src/lib/bbiRead.c
  • 1.8 lines changed: 25, context: html, text, full: html, text
    Adding fieldCount and definedFieldCount to bbiFile header for bigBeds.
• src/lib/bigBed.c
  • 1.10 lines changed: 14, context: html, text, full: html, text
    Adding fieldCount and definedFieldCount to bbiFile header for bigBeds.
• src/lib/bwgQuery.c
  • 1.18 lines changed: 106, context: html, text, full: html, text
    Removing unused code.
• src/lib/udc.c
  • 1.12 lines changed: 56, context: html, text, full: html, text
    Removed flocks which seem to be unneeded. Adding qEncoding to make directory names easier to pursue under Unix.
  • 1.8 lines changed: 23, context: html, text, full: html, text
    Cgi-encoding file names in cache dir.
• src/oneShot/test/test.c
  • 1.34 lines changed: 18, context: html, text, full: html, text
    Testing some fool thing.
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Adding fieldCount and definedFieldCount to bbiFile header for bigBeds.
• src/utils/udcCleanup/udcCleanup.c
  • 1.2 lines changed: 17, context: html, text, full: html, text
    Adding -test flag
• src/utils/wigToBigWig/wigToBigWig.c
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Shortened 'clipDontDie' option to just 'clip'