broad.pda.seq.rap.BuildRatioNullDistribution Member List

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

ANNOTATION	broad.pda.seq.rap.GenomeCommandLineProgram
CONTROL	broad.pda.seq.rap.BuildRatioNullDistribution
COORD_SPACE	broad.pda.seq.rap.GenomeCommandLineProgram
coordinateSpace	broad.pda.seq.rap.GenomeCommandLineProgram	protected
customCommandLineValidation()	broad.pda.seq.rap.GenomeCommandLineProgram	protected
doWork()	broad.pda.seq.rap.BuildRatioNullDistribution	protected
GENE	broad.pda.seq.rap.GenomeCommandLineProgram
getCoordinateSpace()	broad.pda.seq.rap.GenomeCommandLineProgram	protected
getEmptyEmpiricalDistribution()	broad.pda.seq.rap.BuildRatioNullDistribution	static
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
KEEP_INTERMEDIATES	broad.pda.seq.rap.BuildRatioNullDistribution
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.BuildRatioNullDistribution	static
MASK_FILE	broad.pda.seq.rap.GenomeCommandLineProgram
MAX_FRAGMENT_LENGTH	broad.pda.seq.rap.GenomeCommandLineProgram
MIN_MAPPING_QUALITY	broad.pda.seq.rap.GenomeCommandLineProgram
OUTPUT	broad.pda.seq.rap.BuildRatioNullDistribution
OVERLAP	broad.pda.seq.rap.BuildRatioNullDistribution
PCT_MASKED_ALLOWED	broad.pda.seq.rap.GenomeCommandLineProgram
PERMUTATIONS	broad.pda.seq.rap.BuildRatioNullDistribution
QUEUE	broad.pda.seq.rap.BuildRatioNullDistribution
RANDOM_SEED	broad.pda.seq.rap.BuildRatioNullDistribution
REGION	broad.pda.seq.rap.GenomeCommandLineProgram
SIZES	broad.pda.seq.rap.GenomeCommandLineProgram
TARGET	broad.pda.seq.rap.BuildRatioNullDistribution
USAGE	broad.pda.seq.rap.BuildRatioNullDistribution
USE_INTERMEDIATES	broad.pda.seq.rap.BuildRatioNullDistribution
WINDOW	broad.pda.seq.rap.BuildRatioNullDistribution