Commits for kent
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v249_base to v250_preview (2011-03-29 to 2011-04-05) v250
- Utility to print out lines shared by all files (or from a column in all files) seems to work.
- src/utils/linesInAllFiles/linesInAllFiles.c - lines changed 105, context: html, text, full: html, text
- src/utils/linesInAllFiles/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/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionPickGeneSet/regCompanionPickGeneSet.c - lines changed 189, context: html, text, full: html, text
- Adding some stuff to query neighborhood around promoters producing averages across all genes.
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/long.lst - lines changed 44, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c - lines changed 189, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/toWig.awk - lines changed 27, 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.
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c - lines changed 58, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/toWig.awk - lines changed 16, context: html, text, full: html, text
- Program to pick enhancers is starting to go. Still a ways left though.
- src/hg/regulate/companion/regCompanionPickEnhancers/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c - lines changed 170, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionPickEnhancers/test.csh - lines changed 2, 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.
- src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c - lines changed 256, 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/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c - lines changed 35, context: html, text, full: html, text
- 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....
- src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c - lines changed 83, context: html, text, full: html, text
- Adding utility to correlate enahancers and promoters with similar activities.
- src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c - lines changed 234, context: html, text, full: html, text
- Adding utility to calculate entropy of expression vectors.
- src/hg/regulate/companion/regCompanionEntropy/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionEntropy/regCompanionEntropy.c - lines changed 92, 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/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c - lines changed 102, context: html, text, full: html, text
- Updating a comment.
- src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c - lines changed 1, 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/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c - lines changed 137, context: html, text, full: html, text
- src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/test.csh - lines changed 2, context: html, text, full: html, text
- Letting there be another clustered DNAse track with a special details page.
- Generating trackDb.ra for more histone marks, and correcting color on K562 which before was too dark.
- src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c - lines changed 13, context: html, text, full: html, text
- Adding viewLimits to track generator.
- src/hg/regulate/companion/regCompanionGraphVsFixedPoints/toWig.awk - lines changed 14, context: html, text, full: html, text
- Adding another input variant format
- src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c - lines changed 10, 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/correlate/correlate.c - lines changed 12, 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/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/regulate/regStartSampleEmbl/regStartSampleEmbl.c - lines changed 129, 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/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
- Added -invert flag.
- src/hg/utils/bedWeedOverlapping/bedWeedOverlapping.c - lines changed 8, context: html, text, full: html, text
- Making bigWigAverageOverBed use the bigWigValsOnChrom interface.
- src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c - lines changed 49, 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 142, context: html, text, full: html, text
- Adding a new output type and a new column to existing output.
- src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c - lines changed 19, context: html, text, full: html, text
- Adding test case.
- src/utils/bedGeneParts/test.in - lines changed 9, context: html, text, full: html, text
- Adding new utilities to makefile.
- Some debugging added.
- src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c - lines changed 20, context: html, text, full: html, text
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