kent: changes by file

branch to review (2009-11-10 to 2009-11-17) v220

• src/hg/hgTracks/hgTracks.h
  • 1.192 lines changed: 3, context: html, text, full: html, text
    Adding whisker plots.
• src/hg/hgTracks/simpleTracks.c
  • 1.113 lines changed: 7, context: html, text, full: html, text
    Adding whisker plots.
• src/hg/hgTracks/wigCommon.h
  • 1.9 lines changed: 5, context: html, text, full: html, text
    Adding whisker plots.
• src/hg/hgTracks/wigTrack.c
  • 1.96 lines changed: 14, context: html, text, full: html, text
    Making whiskers take light and medium color from primary color rather than always using grays.
  • 1.95 lines changed: 154, context: html, text, full: html, text
    Adding whisker plots.
• src/hg/inc/hui.h
  • 1.142 lines changed: 4, context: html, text, full: html, text
    Adding whisker plots.
• src/hg/lib/hui.c
  • 1.249 lines changed: 3, context: html, text, full: html, text
    Adding whisker plots.
• src/hg/lib/wiggleCart.c
  • 1.25 lines changed: 1, context: html, text, full: html, text
    Initializing some vars to zero to fix compiler warning on older compiler that wasn't quite sophisticated enough to see that these are actually initialized in all paths.
• src/hg/oneShot/freen/freen.c
  • 1.92 lines changed: 7, context: html, text, full: html, text
    More zlib testing.
  • 1.91 lines changed: 10, context: html, text, full: html, text
    Testing zlibFace.
• src/hg/txCds/txCdsRedoUniprotPicks/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Seems to work.
• src/hg/txCds/txCdsRedoUniprotPicks/txCdsRedoUniprotPicks.c
  • 1.1 lines changed: 148, context: html, text, full: html, text
    Seems to work.
• src/inc/bbiFile.h
  • 1.19 lines changed: 21, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
  • 1.18 lines changed: 7, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/inc/bigWig.h
  • 1.13 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/inc/common.h
  • 1.158 lines changed: 15, context: html, text, full: html, text
    Adding a few new utilities to common.h/common.c for benefit of bbi compressed encoders.
• src/inc/dystring.h
  • 1.20 lines changed: 4, context: html, text, full: html, text
    Adding dyStringWriteOne.
• src/inc/zlibFace.h
  • 1.1 lines changed: 26, context: html, text, full: html, text
    Adding zlib interface routines.
• src/lib/bbiRead.c
  • 1.16 lines changed: 3, context: html, text, full: html, text
    Making assumptions of bbiTotalSummary vs. version numbers a bit more explicit in response to Angie's feedback.
  • 1.15 lines changed: 59, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/lib/bbiWrite.c
  • 1.10 lines changed: 75, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
  • 1.9 lines changed: 74, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/lib/bigBed.c
  • 1.23 lines changed: 46, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
• src/lib/bwgCreate.c
  • 1.21 lines changed: 19, context: html, text, full: html, text
    Improving calculations about initial zoom level in wigToBigWig, especially for compressed files.
  • 1.20 lines changed: 125, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/lib/bwgQuery.c
  • 1.23 lines changed: 111, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/lib/cirTree.c
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Removing some commented out debugging statements.
• src/lib/common.c
  • 1.136 lines changed: 33, context: html, text, full: html, text
    Adding a few new utilities to common.h/common.c for benefit of bbi compressed encoders.
• src/lib/dystring.c
  • 1.25 lines changed: 4, context: html, text, full: html, text
    Adding dyStringWriteOne.
• src/lib/gifLabel.c
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Changing uglyf to printf since it's not just a temporary thing.
• src/lib/makefile
  • 1.155 lines changed: 1, context: html, text, full: html, text
    Adding zlib interface routines.
• src/lib/zlibFace.c
  • 1.1 lines changed: 91, context: html, text, full: html, text
    Adding zlib interface routines.
• src/utils/makefile
  • 1.74 lines changed: 1, context: html, text, full: html, text
    Adding new bigWigToWig utility. You won't get _exactly_ the same wig that you gave to wigToBigWig back. It'll omit printing the decimal point in the floating point values when possible, and also it will break up large sections into medium-sized ones. Still at least it keeps fixedStep and varStep rather than converting everything to bedGraph.
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • 1.22 lines changed: 3, context: html, text, full: html, text
    Making compression the default for the bigBed and bigWig creators.
  • 1.21 lines changed: 2, context: html, text, full: html, text
    Fixed bug in sumSquares.
  • 1.20 lines changed: 69, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
  • 1.19 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bedGraphToBigWig/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.20 lines changed: 3, context: html, text, full: html, text
    Making compression the default for the bigBed and bigWig creators.
  • 1.19 lines changed: 2, context: html, text, full: html, text
    Fixed bug in sumSquares.
  • 1.18 lines changed: 61, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
  • 1.17 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bedToBigBed/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigBedInfo/bigBedInfo.c
  • 1.2 lines changed: 26, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
• src/utils/bigBedInfo/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
• src/utils/bigBedSummary/makefile
  • 1.9 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigBedToBed/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigWigInfo/bigWigInfo.c
  • 1.6 lines changed: 21, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
  • 1.5 lines changed: 2, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigWigInfo/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigWigSummary/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigWigToBedGraph/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigWigToWig/bigWigToWig.c
  • 1.1 lines changed: 79, context: html, text, full: html, text
    Adding new bigWigToWig utility. You won't get _exactly_ the same wig that you gave to wigToBigWig back. It'll omit printing the decimal point in the floating point values when possible, and also it will break up large sections into medium-sized ones. Still at least it keeps fixedStep and varStep rather than converting everything to bedGraph.
• src/utils/bigWigToWig/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Adding new bigWigToWig utility. You won't get _exactly_ the same wig that you gave to wigToBigWig back. It'll omit printing the decimal point in the floating point values when possible, and also it will break up large sections into medium-sized ones. Still at least it keeps fixedStep and varStep rather than converting everything to bedGraph.
• src/utils/raToLines/makefile
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Removing unused library.
• src/utils/scaffoldFaToAgp/makefile
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
• src/utils/wigToBigWig/makefile
  • 1.9 lines changed: 2, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/wigToBigWig/wigToBigWig.c
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Making compression the default for the bigBed and bigWig creators.
  • 1.8 lines changed: 10, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/wigToBigWig/expected/tf1.sum
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Updating expected output.
• src/utils/wigToBigWig/expected/tf3.sum
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Updating expected output.