kent: changes by commit
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branch to review (2009-11-10 to 2009-11-17) v220
- 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/lib/wiggleCart.c 1.25 - lines changed: 1, context: html, text, full: html, text
- Testing zlibFace.
- src/hg/oneShot/freen/freen.c 1.91 - lines changed: 10, context: html, text, full: html, text
- Adding zlib interface routines.
- src/inc/zlibFace.h 1.1 - lines changed: 26, context: html, text, full: html, text
- src/lib/makefile 1.155 - lines changed: 1, context: html, text, full: html, text
- src/lib/zlibFace.c 1.1 - lines changed: 91, context: html, text, full: html, text
- Updating expected output.
- src/utils/wigToBigWig/expected/tf1.sum 1.2 - lines changed: 1, context: html, text, full: html, text
- src/utils/wigToBigWig/expected/tf3.sum 1.3 - lines changed: 1, context: html, text, full: html, text
- Seems to work.
- src/hg/txCds/txCdsRedoUniprotPicks/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
- src/hg/txCds/txCdsRedoUniprotPicks/txCdsRedoUniprotPicks.c 1.1 - lines changed: 148, context: html, text, full: html, text
- Changing uglyf to printf since it's not just a temporary thing.
- src/lib/gifLabel.c 1.11 - lines changed: 1, context: html, text, full: html, text
- Adding a few new utilities to common.h/common.c for benefit of bbi compressed encoders.
- src/inc/common.h 1.158 - lines changed: 15, context: html, text, full: html, text
- src/lib/common.c 1.136 - lines changed: 33, context: html, text, full: html, text
- Removing some commented out debugging statements.
- More zlib testing.
- src/hg/oneShot/freen/freen.c 1.92 - 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/bbiFile.h 1.18 - lines changed: 7, context: html, text, full: html, text
- src/inc/bigWig.h 1.13 - lines changed: 1, context: html, text, full: html, text
- src/lib/bbiRead.c 1.15 - lines changed: 59, context: html, text, full: html, text
- src/lib/bbiWrite.c 1.9 - lines changed: 74, context: html, text, full: html, text
- src/lib/bwgCreate.c 1.20 - lines changed: 125, context: html, text, full: html, text
- src/lib/bwgQuery.c 1.23 - lines changed: 111, context: html, text, full: html, text
- src/utils/bedGraphToBigWig/bedGraphToBigWig.c 1.19 - lines changed: 1, context: html, text, full: html, text
- src/utils/bedGraphToBigWig/makefile 1.6 - lines changed: 1, context: html, text, full: html, text
- src/utils/bedToBigBed/bedToBigBed.c 1.17 - lines changed: 1, context: html, text, full: html, text
- src/utils/bedToBigBed/makefile 1.8 - lines changed: 1, context: html, text, full: html, text
- src/utils/bigBedSummary/makefile 1.9 - lines changed: 1, context: html, text, full: html, text
- src/utils/bigBedToBed/makefile 1.8 - lines changed: 1, context: html, text, full: html, text
- src/utils/bigWigInfo/bigWigInfo.c 1.5 - lines changed: 2, context: html, text, full: html, text
- src/utils/bigWigInfo/makefile 1.5 - lines changed: 1, context: html, text, full: html, text
- src/utils/bigWigSummary/makefile 1.8 - lines changed: 1, context: html, text, full: html, text
- src/utils/bigWigToBedGraph/makefile 1.8 - lines changed: 1, context: html, text, full: html, text
- src/utils/wigToBigWig/makefile 1.9 - lines changed: 2, context: html, text, full: html, text
- src/utils/wigToBigWig/wigToBigWig.c 1.8 - lines changed: 10, 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/bigWigToWig.c 1.1 - lines changed: 79, context: html, text, full: html, text
- src/utils/bigWigToWig/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
- src/utils/makefile 1.74 - lines changed: 1, context: html, text, full: html, text
- Removing unused library.
- src/utils/raToLines/makefile 1.4 - lines changed: 1, context: html, text, full: html, text
- Adding dyStringWriteOne.
- src/inc/dystring.h 1.20 - lines changed: 4, context: html, text, full: html, text
- src/lib/dystring.c 1.25 - lines changed: 4, context: html, text, full: html, text
- Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
- src/inc/bbiFile.h 1.19 - lines changed: 21, context: html, text, full: html, text
- src/lib/bbiWrite.c 1.10 - lines changed: 75, context: html, text, full: html, text
- src/lib/bigBed.c 1.23 - lines changed: 46, context: html, text, full: html, text
- src/utils/bedGraphToBigWig/bedGraphToBigWig.c 1.20 - lines changed: 69, context: html, text, full: html, text
- src/utils/bedToBigBed/bedToBigBed.c 1.18 - lines changed: 61, context: html, text, full: html, text
- src/utils/bigBedInfo/bigBedInfo.c 1.2 - lines changed: 26, context: html, text, full: html, text
- src/utils/bigBedInfo/makefile 1.3 - lines changed: 1, context: html, text, full: html, text
- src/utils/bigWigInfo/bigWigInfo.c 1.6 - lines changed: 21, context: html, text, full: html, text
- src/utils/scaffoldFaToAgp/makefile 1.9 - lines changed: 2, context: html, text, full: html, text
- Fixed bug in sumSquares.
- src/utils/bedGraphToBigWig/bedGraphToBigWig.c 1.21 - lines changed: 2, context: html, text, full: html, text
- src/utils/bedToBigBed/bedToBigBed.c 1.19 - lines changed: 2, context: html, text, full: html, text
- Making assumptions of bbiTotalSummary vs. version numbers a bit more explicit in response to Angie's feedback.
- src/lib/bbiRead.c 1.16 - lines changed: 3, context: html, text, full: html, text
- Improving calculations about initial zoom level in wigToBigWig, especially for compressed files.
- src/lib/bwgCreate.c 1.21 - lines changed: 19, context: html, text, full: html, text
- Making compression the default for the bigBed and bigWig creators.
- src/utils/bedGraphToBigWig/bedGraphToBigWig.c 1.22 - lines changed: 3, context: html, text, full: html, text
- src/utils/bedToBigBed/bedToBigBed.c 1.20 - lines changed: 3, context: html, text, full: html, text
- src/utils/wigToBigWig/wigToBigWig.c 1.9 - lines changed: 3, context: html, text, full: html, text
- Adding whisker plots.
- src/hg/hgTracks/hgTracks.h 1.192 - lines changed: 3, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c 1.113 - lines changed: 7, context: html, text, full: html, text
- src/hg/hgTracks/wigCommon.h 1.9 - lines changed: 5, context: html, text, full: html, text
- src/hg/hgTracks/wigTrack.c 1.95 - lines changed: 154, context: html, text, full: html, text
- src/hg/inc/hui.h 1.142 - lines changed: 4, context: html, text, full: html, text
- src/hg/lib/hui.c 1.249 - lines changed: 3, context: html, text, full: html, text
- Making whiskers take light and medium color from primary color rather than always using grays.
- src/hg/hgTracks/wigTrack.c 1.96 - lines changed: 14, context: html, text, full: html, text
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