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

ANNOTATION	broad.pda.seq.rap.GenomeCommandLineProgram
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.ShuffleBED	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
INPUT	broad.pda.seq.rap.ShuffleBED
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.ShuffleBED	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.ShuffleBED
PCT_MASKED_ALLOWED	broad.pda.seq.rap.GenomeCommandLineProgram
PERMUTATIONS	broad.pda.seq.rap.ShuffleBED
REGION	broad.pda.seq.rap.GenomeCommandLineProgram
shuffleAndWriteAnnotations(AnnotationList< Annotation > regions, GenomicSpace cs, AnnotationList<?extends Annotation > annotations, File output, int permutations)	broad.pda.seq.rap.ShuffleBED	static
SIZES	broad.pda.seq.rap.GenomeCommandLineProgram
USAGE	broad.pda.seq.rap.ShuffleBED