File Changes for kent
switch to commits view, user indexv249_preview to v249_preview2 (2011-03-15 to 2011-03-22) v249
- src/hg/hgTracks/factorSource.c
- lines changed 17, context: html, text, full: html, text
Improving packing of factorSource tracks.
- src/hg/hgc/peakClusters.c
- lines changed 114, 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/inc/hui.h
- lines changed 3, context: html, text, full: html, text
Exposing controlledVocabLink, now used outside of module.
- src/hg/lib/clusterInputTrackTable3.as
- lines changed 9, 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.sql
- lines changed 17, 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/clusterInputTrackTable4.as
- lines changed 10, context: html, text, full: html, text
Adding some more varients of clusterInput tracks, with more fields. Hmm, not wild about this proliferation.
- lines changed 1, context: html, text, full: html, text
Changing cell field to cellType to better connect with Encode controlled vocab.
- lines changed 1, context: html, text, full: html, text
Updating 3's to 4's to be consistent and make buildTableDescriptions happy.
- src/hg/lib/clusterInputTrackTable4.sql
- lines changed 18, context: html, text, full: html, text
Adding some more varients of clusterInput tracks, with more fields. Hmm, not wild about this proliferation.
- lines changed 1, context: html, text, full: html, text
Changing cell field to cellType to better connect with Encode controlled vocab.
- lines changed 3, context: html, text, full: html, text
Updating 3's to 4's to be consistent and make buildTableDescriptions happy.
- src/hg/makeDb/doc/hg19.txt
- lines changed 57, context: html, text, full: html, text
Working on figuring out colors for wgEncodeReg rainbow fringe graphs based on clustering cell expression patterns
- lines changed 10, context: html, text, full: html, text
Further work on wgEncodeReg
- lines changed 19, context: html, text, full: html, text
Doing more wgEncodeReg work. This is version put on pushQ initially.
- src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
- lines changed 25, context: html, text, full: html, text
Adding in a check for each source + factor combination being unique.
- src/hg/makeDb/trackDb/README
- lines changed 7, 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/trackDb.wgEncode.ra
- lines changed 3, context: html, text, full: html, text
First cut of ENCODE regulation super track for hg19.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.html
- lines changed 63, context: html, text, full: html, text
Adding description html pages for wgEncodeReg tracks for hg19
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
- lines changed 328, context: html, text, full: html, text
First cut of ENCODE regulation super track for hg19.
- lines changed 8, context: html, text, full: html, text
Moving to V2 Caltech RNA tables.
- lines changed 6, 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
- lines changed 1, context: html, text, full: html, text
Improving scale on wgEncodeRegTxn.
- 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/wgEncodeRegDnaseClustered.html
- lines changed 28, context: html, text, full: html, text
Adding description html pages for wgEncodeReg tracks for hg19
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRegMarkH3k27ac.html
- lines changed 38, context: html, text, full: html, text
Adding description html pages for wgEncodeReg tracks for hg19
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRegMarkH3k4me1.html
- lines changed 37, context: html, text, full: html, text
Adding description html pages for wgEncodeReg tracks for hg19
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRegMarkH3k4me3.html
- lines changed 37, context: html, text, full: html, text
Adding description html pages for wgEncodeReg tracks for hg19
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClustered.html
- lines changed 57, context: html, text, full: html, text
Adding description html pages for wgEncodeReg tracks for hg19
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTxn.html
- lines changed 33, context: html, text, full: html, text
Adding description html pages for wgEncodeReg tracks for hg19
- 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/oneShot/freen/freen.c
- lines changed 195, context: html, text, full: html, text
Making freen make a web page with rainbows derived from Autodesk Animator color map.
- lines changed 59, context: html, text, full: html, text
Adding rainbow generating routines.
- src/hg/oneShot/wgEncodeRegGenRa/makefile
- lines changed 18, context: html, text, full: html, text
A little program to generate parts of trackDb.ra file for wgEncodeReg.
- src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
- lines changed 130, context: html, text, full: html, text
A little program to generate parts of trackDb.ra file for wgEncodeReg.
- src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c
- lines changed 1, context: html, text, full: html, text
Fixing bug Fan found reading my code. Yea!
- src/hg/regulate/regClusterTreeCells/makefile
- src/hg/regulate/regClusterTreeCells/regClusterTreeCells.c
- lines changed 88, context: html, text, full: html, text
Making it use a standard tree output format. Changing to be a binary tree rather than general hierarchy.
- lines changed 28, context: html, text, full: html, text
Adding -short and -rename options
- src/hg/regulate/regClusterTreeCells/tests/expected.tree
- src/hg/regulate/regClusterTreeCells/tests/in.lst
- src/hg/regulate/regClusterTreeCells/tests/in/1.bed
- src/hg/regulate/regClusterTreeCells/tests/in/10.bed
- src/hg/regulate/regClusterTreeCells/tests/in/2.bed
- src/hg/regulate/regClusterTreeCells/tests/in/3.bed
- src/hg/regulate/regClusterTreeCells/tests/in/4.bed
- src/hg/regulate/regClusterTreeCells/tests/in/5.bed
- src/hg/regulate/regClusterTreeCells/tests/in/6.bed
- src/hg/regulate/regClusterTreeCells/tests/in/7.bed
- src/hg/regulate/regClusterTreeCells/tests/in/8.bed
- src/hg/regulate/regClusterTreeCells/tests/in/9.bed
- src/hg/regulate/wgEncodeReg/picksFromDupes.tab
- lines changed 39, context: html, text, full: html, text
Saving away input to cleanup program.
- src/inc/rainbow.h
- lines changed 18, context: html, text, full: html, text
Adding rainbow generating routines.
- src/lib/hash.c
- lines changed 3, context: html, text, full: html, text
Indulging in a little paranoia about void pointer arithmetic.
- src/lib/makefile
- lines changed 2, context: html, text, full: html, text
Adding rainbow generating routines.
- src/lib/rainbow.c
- lines changed 112, context: html, text, full: html, text
Adding rainbow generating routines.
- src/utils/bedCommonRegions/bedCommonRegions.c
- lines changed 120, 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.
- lines changed 24, context: html, text, full: html, text
Adding -removeOverlap flag.
- 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/makefile
- lines changed 22, 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/tests/expected.bed
- lines changed 7, 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/tests/in/1.bed
- lines changed 9, 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/tests/in/2.bed
- lines changed 9, 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/tests/in/3.bed
- lines changed 9, 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/bedRestrictToPositions/bedRestrictToPositions.c
- lines changed 92, context: html, text, full: html, text
Adding another bed cleanup utility.
- src/utils/bedRestrictToPositions/makefile
- lines changed 18, context: html, text, full: html, text
Adding another bed cleanup utility.
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