kent: changes by file

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

• src/hg/hgTracks/bedTrack.c
  • 1.19 lines changed: 7, context: html, text, full: html, text
    Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete.
• src/hg/hgTracks/bigWigTrack.c
  • 1.7 lines changed: 5, context: html, text, full: html, text
    Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete.
• src/hg/hgTracks/hgTracks.c
  • 1.1604 lines changed: 28, context: html, text, full: html, text
    Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete.
• src/hg/hgTracks/hgTracks.h
  • 1.189 lines changed: 11, context: html, text, full: html, text
    Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete.
• src/hg/hgTracks/simpleTracks.c
  • 1.110 lines changed: 9, context: html, text, full: html, text
    Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete.
• src/hg/inc/customTrack.h
  • 1.56 lines changed: 1, context: html, text, full: html, text
    Adding bbiFile field to customTrack to avoid reopening it repeatedly.
• src/hg/lib/customFactory.c
  • 1.110 lines changed: 23, context: html, text, full: html, text
    Adding bbiFile field to customTrack to avoid reopening it repeatedly. Setting display limits from bigWig/bigBed files so they don't end up the weird 0-127 defaults.
• src/hg/lib/wiggleCart.c
  • 1.24 lines changed: 111, context: html, text, full: html, text
    Hopefully making wiggle limits behave a little nicer when defaults are not set. Certainly works nicer with bigWig
• src/hg/oneShot/freen/freen.c
  • 1.90 lines changed: 23, context: html, text, full: html, text
    Testing zlib compress and uncompress.
• src/hg/oneShot/freen/makefile
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Testing zlib compress and uncompress.
• src/inc/bbiFile.h
  • 1.17 lines changed: 3, context: html, text, full: html, text
    adding bbiSummaryElementWrite
  • 1.16 lines changed: 5, context: html, text, full: html, text
    Adding bbiTotalSummary.
  • 1.15 lines changed: 25, context: html, text, full: html, text
    Bumping version number. Making sectionCount and zoomCount more consistent.
• src/inc/bigBed.h
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Making bigWigSummary functions take a bbiFile rather than a fileName.
  • 1.16 lines changed: 3, context: html, text, full: html, text
    Adding bigBedAutoSqlText.
• src/inc/bigWig.h
  • 1.12 lines changed: 5, context: html, text, full: html, text
    Making bigWigSummary functions take a bbiFile rather than a fileName.
• src/inc/udc.h
  • 1.13 lines changed: 3, context: html, text, full: html, text
    Adding udcReadDouble.
  • 1.12 lines changed: 3, context: html, text, full: html, text
    Adding udcReadFloat function.
• src/lib/bbiRead.c
  • 1.14 lines changed: 2, context: html, text, full: html, text
    Updating bbiOpen to handle totalSummary.
  • 1.13 lines changed: 70, context: html, text, full: html, text
    Adding bbiTotalSummary.
• src/lib/bbiWrite.c
  • 1.8 lines changed: 10, context: html, text, full: html, text
    adding bbiSummaryElementWrite
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Bumping version number. Making sectionCount and zoomCount more consistent.
• src/lib/bigBed.c
  • 1.22 lines changed: 12, context: html, text, full: html, text
    Adding bigBedAutoSqlText.
• src/lib/bwgCreate.c
  • 1.19 lines changed: 40, context: html, text, full: html, text
    Adding totalSummary to big files. Should be helpful in quickly calculating ranges to be displayed by default.
  • 1.18 lines changed: 2, context: html, text, full: html, text
    Bumping version number. Making sectionCount and zoomCount more consistent.
• src/lib/bwgQuery.c
  • 1.22 lines changed: 9, context: html, text, full: html, text
    Making bigWigSummary functions take a bbiFile rather than a fileName.
• src/lib/udc.c
  • 1.21 lines changed: 10, context: html, text, full: html, text
    Adding udcReadDouble.
  • 1.20 lines changed: 10, context: html, text, full: html, text
    Adding udcReadFloat function.
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • 1.18 lines changed: 42, context: html, text, full: html, text
    Adding totalSummary to big files. Should be helpful in quickly calculating ranges to be displayed by default.
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Adding version number to usage statement.
  • 1.16 lines changed: 12, context: html, text, full: html, text
    Bumping version number. Making sectionCount and zoomCount more consistent. Also fixing bug with sumSquares being just sum.
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Changing default blockSize and itemsPerSlot to something more reasonable.
  • 1.15 lines changed: 47, context: html, text, full: html, text
    Adding totalSummary to big files. Should be helpful in quickly calculating ranges to be displayed by default.
  • 1.14 lines changed: 4, context: html, text, full: html, text
    Adding version number to usage statement.
  • 1.13 lines changed: 2, context: html, text, full: html, text
    Fixing bug where sumSquares was actually just sum.
  • 1.12 lines changed: 7, context: html, text, full: html, text
    Bumping version number. Making sectionCount and zoomCount more consistent.
• src/utils/bigBedInfo/bigBedInfo.c
  • 1.1 lines changed: 78, context: html, text, full: html, text
    Utility to get information on a bigBed seems to work.
• src/utils/bigBedInfo/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    Utility to get information on a bigBed seems to work.
• src/utils/bigBedInfo/test.bed
  • 1.1 lines changed: 6, context: html, text, full: html, text
    Utility to get information on a bigBed seems to work.
• src/utils/bigWigInfo/bigWigInfo.c
  • 1.4 lines changed: 6, context: html, text, full: html, text
    Adding additional information to bigWigInfo output - data and index sizes.
  • 1.3 lines changed: 11, context: html, text, full: html, text
    Making listing of chromosomes just an option. Adding info from totalSummary, which some day may be used to set min/max values of bigBed/bigWig wiggle ranges.
• src/utils/bigWigSummary/bigWigSummary.c
  • 1.12 lines changed: 4, context: html, text, full: html, text
    Making bigWigSummary functions take a bbiFile rather than a fileName.
• src/utils/wigToBigWig/wigToBigWig.c
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Adding version number to usage statement.