broad.pda.seq.clip.Pileup Member List

This is the complete list of members for broad.pda.seq.clip.Pileup, including all inherited members.

getAnnotation()	broad.pda.seq.clip.Pileup
getFragmentEndsFromBamFile(Annotation region, boolean fullyContained, boolean fivePrimeEnd)	broad.pda.seq.clip.Pileup
getScanPvalFragmentEndsMaxPositionAllRegionsBam(boolean fullyContained, Map< String, Double > nucProbs, int numPermutations, boolean fivePrimeEnd)	broad.pda.seq.clip.Pileup
getScanPvalFragmentEndsMaxPositionBam(Annotation region, boolean fullyContained, Map< String, Double > nucProbs, int numPermutations, boolean fivePrimeEnd)	broad.pda.seq.clip.Pileup
getScanPvalsFragmentEndPileupsAllRegionsWig(boolean fullyContained, Map< String, Double > nucProbs, int numPermutations)	broad.pda.seq.clip.Pileup
getScanPvalsFragmentEndPileupsWig(Annotation region, boolean fullyContained, Map< String, Double > nucProbs, int numPermutations)	broad.pda.seq.clip.Pileup
getShuffledPositions(Annotation region, boolean fullyContained, Map< String, Double > nucProbs, int numPermutations)	broad.pda.seq.clip.Pileup
getShuffledPositionsAllRegions(boolean fullyContained, Map< String, Double > nucProbs, int numPermutations)	broad.pda.seq.clip.Pileup
main(String[] args)	broad.pda.seq.clip.Pileup	static
Pileup(String bamFile, String annotationBedFile, String subregionBedFile, String genomeFasta, Collection< Predicate< Alignment >> readFilters)	broad.pda.seq.clip.Pileup
Pileup(String bamFile, String fragmentEndWig, String annotationBedFile, String subregionBedFile, String genomeFasta, String regionOverlapperCountFile, String peakRegionBedFile, Collection< Predicate< Alignment >> readFilters)	broad.pda.seq.clip.Pileup
writeScanPvalsFragmentEndPileupsAllRegionsWig(String outTable, String outBed, double pvalCutoffForBed, boolean fullyContained, Map< String, Double > nucProbs, int numPermutations)	broad.pda.seq.clip.Pileup