File Changes for kent
switch to commits view, user indexv249_base to v250_preview (2011-03-29 to 2011-04-05) v250
- src/hg/hgc/hgc.c
- lines changed 2, context: html, text, full: html, text
Letting there be another clustered DNAse track with a special details page.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
Putting in commented out line to stuff I'm working on. Trying to be inobtrusive is why it's commented out.
- src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
- lines changed 13, context: html, text, full: html, text
Generating trackDb.ra for more histone marks, and correcting color on K562 which before was too dark.
- src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/makefile
- lines changed 18, context: html, text, full: html, text
Adding utility to correlate enahancers and promoters with similar activities.
- src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c
- lines changed 234, context: html, text, full: html, text
Adding utility to correlate enahancers and promoters with similar activities.
- lines changed 137, context: html, text, full: html, text
Making it have three types of BED outputs. I think I like the third the best.
- lines changed 19, context: html, text, full: html, text
Adding a new output type and a new column to existing output.
- src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/test.csh
- lines changed 2, context: html, text, full: html, text
Making it have three types of BED outputs. I think I like the third the best.
- src/hg/regulate/companion/regCompanionEntropy/makefile
- lines changed 18, context: html, text, full: html, text
Adding utility to calculate entropy of expression vectors.
- src/hg/regulate/companion/regCompanionEntropy/regCompanionEntropy.c
- lines changed 92, context: html, text, full: html, text
Adding utility to calculate entropy of expression vectors.
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/long.lst
- lines changed 44, context: html, text, full: html, text
Adding some stuff to query neighborhood around promoters producing averages across all genes.
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/makefile
- lines changed 18, context: html, text, full: html, text
Adding some stuff to query neighborhood around promoters producing averages across all genes.
- lines changed 1, context: html, text, full: html, text
Making it take an input table with clamping values, how-to-handle-missing-zeroes on a file-by-file basis.
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c
- lines changed 189, context: html, text, full: html, text
Adding some stuff to query neighborhood around promoters producing averages across all genes.
- lines changed 58, context: html, text, full: html, text
Adding -missingZero and -maxVal flags to improve Caltech RNA results. Reworking plus/minus strand logic so there's less duplication of code.
- lines changed 35, context: html, text, full: html, text
Making a chromosome-at-a-time access object for bigWigs. Had repeated this code 3 times, so it's time....
- lines changed 102, context: html, text, full: html, text
Making it take an input table with clamping values, how-to-handle-missing-zeroes on a file-by-file basis.
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/toWig.awk
- lines changed 27, context: html, text, full: html, text
Adding some stuff to query neighborhood around promoters producing averages across all genes.
- lines changed 16, context: html, text, full: html, text
Adding -missingZero and -maxVal flags to improve Caltech RNA results. Reworking plus/minus strand logic so there's less duplication of code.
- lines changed 14, context: html, text, full: html, text
Adding viewLimits to track generator.
- src/hg/regulate/companion/regCompanionPickEnhancers/makefile
- lines changed 18, context: html, text, full: html, text
Program to pick enhancers is starting to go. Still a ways left though.
- src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c
- lines changed 170, context: html, text, full: html, text
Program to pick enhancers is starting to go. Still a ways left though.
- lines changed 256, context: html, text, full: html, text
Seems to be picking an interesting set. Some browsing suggests that the number of calls are a little conservative, but that's ok.
- lines changed 83, context: html, text, full: html, text
Making a chromosome-at-a-time access object for bigWigs. Had repeated this code 3 times, so it's time....
- src/hg/regulate/companion/regCompanionPickEnhancers/test.csh
- lines changed 2, context: html, text, full: html, text
Program to pick enhancers is starting to go. Still a ways left though.
- src/hg/regulate/companion/regCompanionPickGeneSet/makefile
- lines changed 18, context: html, text, full: html, text
Committing a half-abandoned attempt at a gene picker for the companion paper in C to replace scripts I was using. May come back to it later.
- src/hg/regulate/companion/regCompanionPickGeneSet/regCompanionPickGeneSet.c
- lines changed 189, context: html, text, full: html, text
Committing a half-abandoned attempt at a gene picker for the companion paper in C to replace scripts I was using. May come back to it later.
- src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
- lines changed 10, context: html, text, full: html, text
Adding another input variant format
- src/hg/regulate/regStartSampleEmbl/makefile
- lines changed 18, context: html, text, full: html, text
A little utility to make a template EMBL file for annotating regulatory regions by hand.
- src/hg/regulate/regStartSampleEmbl/regStartSampleEmbl.c
- lines changed 129, context: html, text, full: html, text
A little utility to make a template EMBL file for annotating regulatory regions by hand.
- src/hg/utils/bedWeedOverlapping/bedWeedOverlapping.c
- src/inc/bigWig.h
- lines changed 27, context: html, text, full: html, text
Making a chromosome-at-a-time access object for bigWigs. Had repeated this code 3 times, so it's time....
- lines changed 11, context: html, text, full: html, text
Having bigWigValsOnChromFetchData read bigWig directly rather than going through bigWigIntervalQuery in hopes of speeding up particularly on things that have a value for each base and are stored as fixedStep. It does speed it up by 2x when you are not too i/o bound.
- src/inc/bwgInternal.h
- lines changed 16, context: html, text, full: html, text
Having bigWigValsOnChromFetchData read bigWig directly rather than going through bigWigIntervalQuery in hopes of speeding up particularly on things that have a value for each base and are stored as fixedStep. It does speed it up by 2x when you are not too i/o bound.
- src/lib/bwgQuery.c
- lines changed 13, context: html, text, full: html, text
Having bigWigValsOnChromFetchData read bigWig directly rather than going through bigWigIntervalQuery in hopes of speeding up particularly on things that have a value for each base and are stored as fixedStep. It does speed it up by 2x when you are not too i/o bound.
- src/lib/bwgValsOnChrom.c
- lines changed 72, context: html, text, full: html, text
Making a chromosome-at-a-time access object for bigWigs. Had repeated this code 3 times, so it's time....
- lines changed 142, context: html, text, full: html, text
Having bigWigValsOnChromFetchData read bigWig directly rather than going through bigWigIntervalQuery in hopes of speeding up particularly on things that have a value for each base and are stored as fixedStep. It does speed it up by 2x when you are not too i/o bound.
- src/lib/makefile
- lines changed 1, context: html, text, full: html, text
Making a chromosome-at-a-time access object for bigWigs. Had repeated this code 3 times, so it's time....
- src/utils/bedGeneParts/test.in
- src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c
- lines changed 49, context: html, text, full: html, text
Making bigWigAverageOverBed use the bigWigValsOnChrom interface.
- src/utils/correlate/correlate.c
- lines changed 12, context: html, text, full: html, text
Making it so that for this command line utility '1' rather than '0' refers to the first column, which is more consistent with other command line utilities.
- src/utils/linesInAllFiles/linesInAllFiles.c
- lines changed 105, context: html, text, full: html, text
Utility to print out lines shared by all files (or from a column in all files) seems to work.
- src/utils/linesInAllFiles/makefile
- lines changed 18, context: html, text, full: html, text
Utility to print out lines shared by all files (or from a column in all files) seems to work.
- src/utils/makefile
- lines changed 6, context: html, text, full: html, text
Adding new utilities to makefile.
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