File Changes for kent

v250_base to v251_preview (2011-04-19 to 2011-04-26) v251

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 0, context: html, text, full: html, text
    Fixed indentation on one line.
• src/hg/hgTracks/bamTrack.c
  • lines changed 9, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 1, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/bedGraph.c
  • lines changed 25, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 6, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 10, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 42, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/container.c
  • lines changed 4, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 1, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/multiWig.c
  • lines changed 21, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 65, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/wigCommon.h
  • lines changed 8, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 4, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/wigTrack.c
  • lines changed 60, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 37, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/htdocs/ENCODE/dataStandards.html
  • lines changed 8, context: html, text, full: html, text
    Removing a link to old standards doc that Barb Wold said was bad bad bad.
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
• src/hg/inc/wiggle.h
  • lines changed 7, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
• src/hg/lib/wiggleCart.c
  • lines changed 49, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    Adding an unfortunately long line that describes how the metadata was faked for the pooled RNA track.
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • lines changed 21, context: html, text, full: html, text
    Updating blastTabs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding metadata for pooled Caltech signals used in wgEncodeReg.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra
  • lines changed 154, context: html, text, full: html, text
    Adding metadata for pooled Caltech signals used in wgEncodeReg.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 11, context: html, text, full: html, text
    Taking configuration off of the short labels. Making table and track names match for the normalized tracks, since part of ENCODE metadata system depends on table being a track in some track.
• src/hg/oneShot/freen/freen.c
  • lines changed 6, context: html, text, full: html, text
    Freen tests timing of opening files.
• src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
  • lines changed 14, context: html, text, full: html, text
    Adding a few more histone marks and a scale.
• src/hg/regulate/companion/regCompanion5C/makefile
  • lines changed 18, context: html, text, full: html, text
    Starting on program to work with 5C data. Seems to read in matrix file ok now.
• src/hg/regulate/companion/regCompanion5C/regCompanion5C.c
  • lines changed 213, context: html, text, full: html, text
    Starting on program to work with 5C data. Seems to read in matrix file ok now.
  • lines changed 58, context: html, text, full: html, text
    Making it produce a bed file with all the same-chromosome pairs over threshold.
  • lines changed 2, context: html, text, full: html, text
    Very minor tweaks.
• src/hg/regulate/companion/regCompanionChia/regCompanionChia.c
  • lines changed 17, context: html, text, full: html, text
    Moving one of the hardcoded files to the command line.
• src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c
  • lines changed 116, context: html, text, full: html, text
    Adding a proper score field from enhancer pick rather than just passing on DNAse score.
• src/hg/regulate/regBeadPos/makefile
  • lines changed 18, context: html, text, full: html, text
    Starting to work on a HMM that positions DNAse relative to a histone
• src/hg/regulate/regBeadPos/regBeadPos.c
  • lines changed 257, context: html, text, full: html, text
    Starting to work on a HMM that positions DNAse relative to a histone
  • lines changed 323, context: html, text, full: html, text
    Manages to produce completely incorrect output without crashing.
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    Seems to emit something worth converting to bed at any rate.
  • lines changed 59, context: html, text, full: html, text
    Refactoring towards making bed output possible.
  • lines changed 124, context: html, text, full: html, text
    Did a bunch of testing. Seems to work.
  • lines changed 31, context: html, text, full: html, text
    Constant tweaking of parameters by hand. Probably best to call it good enough.
  • lines changed 262, context: html, text, full: html, text
    Added capability to output summaries along most likely path and use this to define emission probs. Simplified model just to allow low state, or DNAse flaked by histone.
  • lines changed 152, context: html, text, full: html, text
    Making HMM model simpler and adding some new output types.
• src/hg/regulate/regBeadPos/test.csh
  • lines changed 1, context: html, text, full: html, text
    Did a bunch of testing. Seems to work.
  • lines changed 2, context: html, text, full: html, text
    Added capability to output summaries along most likely path and use this to define emission probs. Simplified model just to allow low state, or DNAse flaked by histone.
  • lines changed 1, context: html, text, full: html, text
    Making HMM model simpler and adding some new output types.
• src/hg/regulate/regBeadPos/test.in
  • lines changed 2, context: html, text, full: html, text
    Did a bunch of testing. Seems to work.
• src/lib/udc.c
  • lines changed 6, context: html, text, full: html, text
    Streamlining transparent case a little.
• src/utils/bedGeneParts/bedGeneParts.c
  • lines changed 2, context: html, text, full: html, text
    Adding missing quotes to usage statement.
• src/utils/bigWigMerge/bigWigMerge.c
  • lines changed 11, context: html, text, full: html, text
    Adding clipping options.
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding test to makefile.
• src/utils/wigCorrelate/wigCorrelate.c
  • lines changed 1, context: html, text, full: html, text
    Removing commented out line of code.