Commits for kent

v249_preview to v249_preview2 (2011-03-15 to 2011-03-22) v249

• Making it use a standard tree output format. Changing to be a binary tree rather than general hierarchy.
  • src/hg/regulate/regClusterTreeCells/regClusterTreeCells.c - lines changed 88, context: html, text, full: html, text
• Adding test set.
  • src/hg/regulate/regClusterTreeCells/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/expected.tree - lines changed 1, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in.lst - lines changed 10, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in/1.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in/10.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in/2.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in/3.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in/4.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in/5.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in/6.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in/7.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in/8.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/regulate/regClusterTreeCells/tests/in/9.bed - lines changed 10, context: html, text, full: html, text
• Making a little utility to extract common regions from bed files. Not bulletproof, but should abort on input it can't handle 99% of the time, and limitations are stated in usage.
  • src/utils/bedCommonRegions/bedCommonRegions.c - lines changed 120, context: html, text, full: html, text
  • src/utils/bedCommonRegions/makefile - lines changed 22, context: html, text, full: html, text
  • src/utils/bedCommonRegions/tests/expected.bed - lines changed 7, context: html, text, full: html, text
  • src/utils/bedCommonRegions/tests/in/1.bed - lines changed 9, context: html, text, full: html, text
  • src/utils/bedCommonRegions/tests/in/2.bed - lines changed 9, context: html, text, full: html, text
  • src/utils/bedCommonRegions/tests/in/3.bed - lines changed 9, context: html, text, full: html, text
• Adding -removeOverlap flag.
  • src/utils/bedCommonRegions/bedCommonRegions.c - lines changed 24, context: html, text, full: html, text
• Removing removeOverlaps flag since under larger scale testing didn't work, and it looked to be a scary pipeline mode problem.
  • src/utils/bedCommonRegions/bedCommonRegions.c - lines changed 24, context: html, text, full: html, text
• Adding another bed cleanup utility.
  • src/utils/bedRestrictToPositions/bedRestrictToPositions.c - lines changed 92, context: html, text, full: html, text
  • src/utils/bedRestrictToPositions/makefile - lines changed 18, context: html, text, full: html, text
• Adding -short and -rename options
  • src/hg/regulate/regClusterTreeCells/regClusterTreeCells.c - lines changed 28, context: html, text, full: html, text
• Adding distances output
  • src/hg/regulate/regClusterTreeCells/regClusterTreeCells.c - lines changed 55, context: html, text, full: html, text
• Indulging in a little paranoia about void pointer arithmetic.
  • src/lib/hash.c - lines changed 3, context: html, text, full: html, text
• Working on figuring out colors for wgEncodeReg rainbow fringe graphs based on clustering cell expression patterns
  • src/hg/makeDb/doc/hg19.txt - lines changed 57, context: html, text, full: html, text
• Making freen make a web page with rainbows derived from Autodesk Animator color map.
  • src/hg/oneShot/freen/freen.c - lines changed 195, context: html, text, full: html, text
• Adding rainbow generating routines.
  • src/hg/oneShot/freen/freen.c - lines changed 59, context: html, text, full: html, text
  • src/inc/rainbow.h - lines changed 18, context: html, text, full: html, text
  • src/lib/makefile - lines changed 2, context: html, text, full: html, text
  • src/lib/rainbow.c - lines changed 112, context: html, text, full: html, text
• A little program to generate parts of trackDb.ra file for wgEncodeReg.
  • src/hg/oneShot/wgEncodeRegGenRa/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c - lines changed 130, context: html, text, full: html, text
• Tweaking and debugging.
  • src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c - lines changed 9, context: html, text, full: html, text
• First cut of ENCODE regulation super track for hg19.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 328, context: html, text, full: html, text
• Moving to V2 Caltech RNA tables.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 8, context: html, text, full: html, text
• Improving packing of factorSource tracks.
  • src/hg/hgTracks/factorSource.c - lines changed 17, context: html, text, full: html, text
• Adding lab column
  • src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c - lines changed 15, context: html, text, full: html, text
• Adding some more varients of clusterInput tracks, with more fields. Hmm, not wild about this proliferation.
  • src/hg/lib/clusterInputTrackTable3.as - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/clusterInputTrackTable3.sql - lines changed 17, context: html, text, full: html, text
  • src/hg/lib/clusterInputTrackTable4.as - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/clusterInputTrackTable4.sql - lines changed 18, context: html, text, full: html, text
• Changing cell field to cellType to better connect with Encode controlled vocab.
  • src/hg/lib/clusterInputTrackTable4.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/clusterInputTrackTable4.sql - lines changed 1, context: html, text, full: html, text
• Exposing controlledVocabLink, now used outside of module.
  • src/hg/inc/hui.h - lines changed 3, context: html, text, full: html, text
• Making it so factorSource tracks can list hits and misses based on the table of inputs rather than relying on the trackDb system. Needed now that integrated regulatory TFBS track is based on data not in other tracks yet.
  • src/hg/hgc/peakClusters.c - lines changed 114, context: html, text, full: html, text
• Adding a new tag so can select fields to display from input table instead of groups to display from trackDb in factorSource type tracks such as wgEncodeRegTfbs
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• Adding a new tag so can select fields to display from input table instead of groups to display from trackDb in factorSource type tracks such as wgEncodeRegTfbs
  • src/hg/makeDb/trackDb/README - lines changed 7, context: html, text, full: html, text
• Further work on wgEncodeReg
  • src/hg/makeDb/doc/hg19.txt - lines changed 10, context: html, text, full: html, text
• Saving away input to cleanup program.
  • src/hg/regulate/wgEncodeReg/picksFromDupes.tab - lines changed 39, context: html, text, full: html, text
• Updating 3's to 4's to be consistent and make buildTableDescriptions happy.
  • src/hg/lib/clusterInputTrackTable4.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/clusterInputTrackTable4.sql - lines changed 3, context: html, text, full: html, text
• Adding description html pages for wgEncodeReg tracks for hg19
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClustered.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegMarkH3k27ac.html - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegMarkH3k4me1.html - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegMarkH3k4me3.html - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClustered.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTxn.html - lines changed 33, context: html, text, full: html, text
• Doing more wgEncodeReg work. This is version put on pushQ initially.
  • src/hg/makeDb/doc/hg19.txt - lines changed 19, context: html, text, full: html, text
• Adding in a check for each source + factor combination being unique.
  • src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c - lines changed 25, context: html, text, full: html, text
• Improving scale on wgEncodeRegTxn.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 1, context: html, text, full: html, text
• Fixing bug Fan found reading my code. Yea!
  • src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c - lines changed 1, context: html, text, full: html, text
• Making HSMM color green in transcription like it is in the histones.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 1, context: html, text, full: html, text