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

ANNOTATION	broad.pda.seq.rap.GenomeCommandLineProgram
CONTROL	broad.pda.seq.rap.RatioPermutationPeakCaller
COORD_SPACE	broad.pda.seq.rap.GenomeCommandLineProgram
coordinateSpace	broad.pda.seq.rap.GenomeCommandLineProgram	protected
customCommandLineValidation()	broad.pda.seq.rap.GenomeCommandLineProgram	protected
CUTOFF	broad.pda.seq.rap.RatioPermutationPeakCaller
DEPLETED	broad.pda.seq.rap.RatioPermutationPeakCaller
doWork()	broad.pda.seq.rap.RatioPermutationPeakCaller	protected
GENE	broad.pda.seq.rap.GenomeCommandLineProgram
getCoordinateSpace()	broad.pda.seq.rap.GenomeCommandLineProgram	protected
getGenes()	broad.pda.seq.rap.GenomeCommandLineProgram
getRegions()	broad.pda.seq.rap.GenomeCommandLineProgram
getRegionSet()	broad.pda.seq.rap.GenomeCommandLineProgram
getRegionsMap()	broad.pda.seq.rap.GenomeCommandLineProgram
isGenomicSpace()	broad.pda.seq.rap.GenomeCommandLineProgram
loadAlignmentModel(File bamFile)	broad.pda.seq.rap.GenomeCommandLineProgram
loadAlignmentModel(File bamFile, boolean pairedEnd)	broad.pda.seq.rap.GenomeCommandLineProgram
loadCoordinateSpace()	broad.pda.seq.rap.GenomeCommandLineProgram	protected
main(final String[] args)	broad.pda.seq.rap.RatioPermutationPeakCaller	static
MASK_FILE	broad.pda.seq.rap.GenomeCommandLineProgram
MAX_FRAGMENT_LENGTH	broad.pda.seq.rap.GenomeCommandLineProgram
MIN_MAPPING_QUALITY	broad.pda.seq.rap.GenomeCommandLineProgram
NULL_DIST	broad.pda.seq.rap.RatioPermutationPeakCaller
OUTPUT	broad.pda.seq.rap.RatioPermutationPeakCaller
OVERLAP	broad.pda.seq.rap.RatioPermutationPeakCaller
PCT_MASKED_ALLOWED	broad.pda.seq.rap.GenomeCommandLineProgram
REGION	broad.pda.seq.rap.GenomeCommandLineProgram
SIZES	broad.pda.seq.rap.GenomeCommandLineProgram
TARGET	broad.pda.seq.rap.RatioPermutationPeakCaller
TRIM	broad.pda.seq.rap.RatioPermutationPeakCaller
USAGE	broad.pda.seq.rap.RatioPermutationPeakCaller
WINDOW	broad.pda.seq.rap.RatioPermutationPeakCaller