Commits for kent

v258_base to v259_preview (2011-10-10 to 2011-10-25) v259

• Adding little utility to help create rainbows and pastel rainbows.
  • src/utils/makeRgbRainbow/makeRgbRainbow.c - lines changed 67, context: html, text, full: html, text
  • src/utils/makeRgbRainbow/makefile - lines changed 18, context: html, text, full: html, text
• Little program that is enough faster and more reliable than awk script to be worthwhile. Figures out factor to get signal to add up to 10 billion.
  • src/hg/regulate/companion/regCompanionCalcBedGraphNorm/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/regulate/companion/regCompanionCalcBedGraphNorm/regCompanionCalcBedGraphNorm.c - lines changed 59, context: html, text, full: html, text
• Adding bedOut option to make output bed that is echo of input bed but with mean column appended
  • src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c - lines changed 31, context: html, text, full: html, text
• Adding sampleAroundCenter option.
  • src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c - lines changed 25, context: html, text, full: html, text
• Adding scoreCol option.
  • src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c - lines changed 13, context: html, text, full: html, text
• Adding a program to help separate enhancer promoter pairs into the cell lines where they are active.
  • src/hg/regulate/companion/regCompanionEnhProCellSpecificPairs/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/regulate/companion/regCompanionEnhProCellSpecificPairs/regCompanionEnhProCellSpecificPairs.c - lines changed 187, context: html, text, full: html, text
• Adding utility to generate random bed files with items of a given size.
  • src/hg/utils/bedRandom/bedRandom.c - lines changed 112, context: html, text, full: html, text
  • src/hg/utils/bedRandom/makefile - lines changed 18, context: html, text, full: html, text
• Fixing missing score field.
  • src/hg/utils/bedRandom/bedRandom.c - lines changed 1, context: html, text, full: html, text
• Adding a program to experiment with a more flexible color overlay system.
  • src/hg/oneShot/tryNewColorOverlay/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/oneShot/tryNewColorOverlay/tryNewColorOverlay.c - lines changed 273, context: html, text, full: html, text
• Updating caltech RNA pooled with a couple of new cell lines.
  • src/hg/makeDb/doc/hg19.txt - lines changed 34, context: html, text, full: html, text
  • src/isPcr/isPcr/isPcr.c - lines changed 1, context: html, text, full: html, text
• Making a utility to compare two lists of IDs.
  • src/utils/vennIds/makefile - lines changed 18, context: html, text, full: html, text
  • src/utils/vennIds/test1 - lines changed 1, context: html, text, full: html, text
  • src/utils/vennIds/test2 - lines changed 1, context: html, text, full: html, text
  • src/utils/vennIds/vennIds.c - lines changed 124, context: html, text, full: html, text
• Fixed comment, chromosome isn't used in this function.
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
• Adding -addId option
  • src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c - lines changed 11, context: html, text, full: html, text
• Adding some verbose status messages.
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 4, context: html, text, full: html, text
• Adding hepG2 and hela cell lines to wgRegEncode track.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra - lines changed 58, context: html, text, full: html, text
• Adding in a couple of more cell lines and spreading out colors a bit to accommodate them.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 54, context: html, text, full: html, text
• Adding hepG2 and hela cell lines to wgRegEncode track.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegNorm.ra - lines changed 256, context: html, text, full: html, text
• Adding -readOnly option.
  • src/hg/oneShot/cartSimNoInsert/cartSimNoInsert.c - lines changed 5, context: html, text, full: html, text
• Some experiments with color.
  • src/hg/oneShot/freen/freen.c - lines changed 49, context: html, text, full: html, text
• Adding two new cell lines.
  • src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c - lines changed 7, context: html, text, full: html, text
• Simplifying name handling in bed file.
  • src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c - lines changed 3, context: html, text, full: html, text
• Adding scoreColIx option
  • src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c - lines changed 15, context: html, text, full: html, text
• Adding hashElCmpWithEmbeddedNumbers.
  • src/inc/hash.h - lines changed 4, context: html, text, full: html, text
  • src/lib/hash.c - lines changed 9, context: html, text, full: html, text
• Adding some constants for hue/sat/value color spaces.
  • src/inc/memgfx.h - lines changed 2, context: html, text, full: html, text
• DOcumenting little bug fix.
  • src/isPcr/version.doc - lines changed 1, context: html, text, full: html, text
• More color experiments hopefully that will result eventually in rainbow fringe graphs that work with more cell lines.
  • src/lib/rainbow.c - lines changed 105, context: html, text, full: html, text