kent: changes by commit

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

• Adding udcReadFloat function.
  • src/inc/udc.h 1.12 - lines changed: 3, context: html, text, full: html, text
  • src/lib/udc.c 1.20 - lines changed: 10, context: html, text, full: html, text
• Adding bigBedAutoSqlText.
  • src/inc/bigBed.h 1.16 - lines changed: 3, context: html, text, full: html, text
  • src/lib/bigBed.c 1.22 - lines changed: 12, context: html, text, full: html, text
• Bumping version number. Making sectionCount and zoomCount more consistent.
  • src/inc/bbiFile.h 1.15 - lines changed: 25, context: html, text, full: html, text
  • src/lib/bbiWrite.c 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/lib/bwgCreate.c 1.18 - lines changed: 2, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c 1.12 - lines changed: 7, 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/bedGraphToBigWig/bedGraphToBigWig.c 1.16 - lines changed: 12, context: html, text, full: html, text
• Adding udcReadDouble.
  • src/inc/udc.h 1.13 - lines changed: 3, context: html, text, full: html, text
  • src/lib/udc.c 1.21 - lines changed: 10, context: html, text, full: html, text
• Adding bbiTotalSummary.
  • src/inc/bbiFile.h 1.16 - lines changed: 5, context: html, text, full: html, text
  • src/lib/bbiRead.c 1.13 - lines changed: 70, 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/bigWigInfo/bigWigInfo.c 1.3 - lines changed: 11, context: html, text, full: html, text
• Utility to get information on a bigBed seems to work.
  • src/utils/bigBedInfo/bigBedInfo.c 1.1 - lines changed: 78, context: html, text, full: html, text
  • src/utils/bigBedInfo/makefile 1.1 - lines changed: 14, context: html, text, full: html, text
  • src/utils/bigBedInfo/test.bed 1.1 - lines changed: 6, context: html, text, full: html, text
• Fixing bug where sumSquares was actually just sum.
  • src/utils/bedToBigBed/bedToBigBed.c 1.13 - lines changed: 2, context: html, text, full: html, text
• Adding version number to usage statement.
  • src/utils/bedGraphToBigWig/bedGraphToBigWig.c 1.17 - lines changed: 2, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c 1.14 - lines changed: 4, context: html, text, full: html, text
  • src/utils/wigToBigWig/wigToBigWig.c 1.7 - lines changed: 3, context: html, text, full: html, text
• adding bbiSummaryElementWrite
  • src/inc/bbiFile.h 1.17 - lines changed: 3, context: html, text, full: html, text
  • src/lib/bbiWrite.c 1.8 - lines changed: 10, context: html, text, full: html, text
• Updating bbiOpen to handle totalSummary.
  • src/lib/bbiRead.c 1.14 - lines changed: 2, context: html, text, full: html, text
• Adding additional information to bigWigInfo output - data and index sizes.
  • src/utils/bigWigInfo/bigWigInfo.c 1.4 - lines changed: 6, context: html, text, full: html, text
• Adding totalSummary to big files. Should be helpful in quickly calculating ranges to be displayed by default.
  • src/lib/bwgCreate.c 1.19 - lines changed: 40, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/bedGraphToBigWig.c 1.18 - lines changed: 42, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c 1.15 - lines changed: 47, context: html, text, full: html, text
• Testing zlib compress and uncompress.
  • src/hg/oneShot/freen/freen.c 1.90 - lines changed: 23, context: html, text, full: html, text
  • src/hg/oneShot/freen/makefile 1.19 - lines changed: 1, context: html, text, full: html, text
• Adding bbiFile field to customTrack to avoid reopening it repeatedly.
  • 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. Setting display limits from bigWig/bigBed files so they don't end up the weird 0-127 defaults.
  • src/hg/lib/customFactory.c 1.110 - lines changed: 23, 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/lib/wiggleCart.c 1.24 - lines changed: 111, context: html, text, full: html, text
• Making bigWigSummary functions take a bbiFile rather than a fileName.
  • src/inc/bigBed.h 1.17 - lines changed: 2, context: html, text, full: html, text
  • src/inc/bigWig.h 1.12 - lines changed: 5, context: html, text, full: html, text
  • src/lib/bwgQuery.c 1.22 - lines changed: 9, context: html, text, full: html, text
  • src/utils/bigWigSummary/bigWigSummary.c 1.12 - lines changed: 4, context: html, text, full: html, text
• Changing default blockSize and itemsPerSlot to something more reasonable.
  • src/utils/bedToBigBed/bedToBigBed.c 1.16 - lines changed: 2, 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/bedTrack.c 1.19 - lines changed: 7, context: html, text, full: html, text
  • src/hg/hgTracks/bigWigTrack.c 1.7 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c 1.1604 - lines changed: 28, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.189 - lines changed: 11, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.110 - lines changed: 9, context: html, text, full: html, text