Commits for kent

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

• Starting on program to work with 5C data. Seems to read in matrix file ok now.
  • src/hg/regulate/companion/regCompanion5C/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/regulate/companion/regCompanion5C/regCompanion5C.c - lines changed 213, context: html, text, full: html, text
• Making it produce a bed file with all the same-chromosome pairs over threshold.
  • src/hg/regulate/companion/regCompanion5C/regCompanion5C.c - lines changed 58, context: html, text, full: html, text
• Starting to work on a HMM that positions DNAse relative to a histone
  • src/hg/regulate/regBeadPos/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/regulate/regBeadPos/regBeadPos.c - lines changed 257, context: html, text, full: html, text
• Manages to produce completely incorrect output without crashing.
  • src/hg/regulate/regBeadPos/regBeadPos.c - lines changed 323, context: html, text, full: html, text
• Seems to emit something worth converting to bed at any rate.
  • src/hg/regulate/regBeadPos/regBeadPos.c - lines changed 30, context: html, text, full: html, text
• Refactoring towards making bed output possible.
  • src/hg/regulate/regBeadPos/regBeadPos.c - lines changed 59, context: html, text, full: html, text
• Did a bunch of testing. Seems to work.
  • src/hg/regulate/regBeadPos/regBeadPos.c - lines changed 124, context: html, text, full: html, text
  • src/hg/regulate/regBeadPos/test.csh - lines changed 1, context: html, text, full: html, text
• Did a bunch of testing. Seems to work.
  • src/hg/regulate/regBeadPos/test.in - lines changed 2, context: html, text, full: html, text
• Constant tweaking of parameters by hand. Probably best to call it good enough.
  • src/hg/regulate/regBeadPos/regBeadPos.c - lines changed 31, 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.
  • src/hg/regulate/regBeadPos/regBeadPos.c - lines changed 262, context: html, text, full: html, text
  • src/hg/regulate/regBeadPos/test.csh - lines changed 2, context: html, text, full: html, text
• Moving one of the hardcoded files to the command line.
  • src/hg/regulate/companion/regCompanionChia/regCompanionChia.c - lines changed 17, context: html, text, full: html, text
• Adding a proper score field from enhancer pick rather than just passing on DNAse score.
  • src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c - lines changed 116, context: html, text, full: html, text
• Making HMM model simpler and adding some new output types.
  • src/hg/regulate/regBeadPos/regBeadPos.c - lines changed 152, context: html, text, full: html, text
  • src/hg/regulate/regBeadPos/test.csh - lines changed 1, context: html, text, full: html, text
• Adding missing quotes to usage statement.
  • src/utils/bedGeneParts/bedGeneParts.c - lines changed 2, context: html, text, full: html, text
• Adding clipping options.
  • src/utils/bigWigMerge/bigWigMerge.c - lines changed 11, context: html, text, full: html, text
• Adding test to makefile.
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
• Removing commented out line of code.
  • src/utils/wigCorrelate/wigCorrelate.c - lines changed 1, context: html, text, full: html, text
• Updating blastTabs
  • src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh - 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.
  • src/hg/hgTracks/bamTrack.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgTracks/bedGraph.c - lines changed 25, context: html, text, full: html, text
  • src/hg/hgTracks/bigWigTrack.c - lines changed 10, context: html, text, full: html, text
  • src/hg/hgTracks/container.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/multiWig.c - lines changed 21, context: html, text, full: html, text
  • src/hg/hgTracks/wigCommon.h - lines changed 8, context: html, text, full: html, text
  • src/hg/hgTracks/wigTrack.c - lines changed 60, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/wiggle.h - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/wiggleCart.c - lines changed 49, 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/bamTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/bedGraph.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hgTracks/bigWigTrack.c - lines changed 42, context: html, text, full: html, text
  • src/hg/hgTracks/multiWig.c - lines changed 65, context: html, text, full: html, text
  • src/hg/hgTracks/wigCommon.h - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/wigTrack.c - 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/hgTracks/hgTracks.h - lines changed 1, context: html, text, full: html, text
• Streamlining transparent case a little.
  • src/lib/udc.c - lines changed 6, context: html, text, full: html, text
• Removing a link to old standards doc that Barb Wold said was bad bad bad.
  • src/hg/htdocs/ENCODE/dataStandards.html - lines changed 8, context: html, text, full: html, text
• Freen tests timing of opening files.
  • src/hg/oneShot/freen/freen.c - lines changed 6, context: html, text, full: html, text
• Adding a few more histone marks and a scale.
  • src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c - lines changed 14, context: html, text, full: html, text
• Very minor tweaks.
  • src/hg/regulate/companion/regCompanion5C/regCompanion5C.c - lines changed 2, context: html, text, full: html, text
• Adding metadata for pooled Caltech signals used in wgEncodeReg.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra - lines changed 154, context: html, text, full: html, text
• Fixed indentation on one line.
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• 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/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 11, 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/hg19.txt - lines changed 4, context: html, text, full: html, text