File Changes for kent

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

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