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broad.pda.seq.rap.ShuffleBAM Member List

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

ANNOTATIONbroad.pda.seq.rap.GenomeCommandLineProgram
COORD_SPACEbroad.pda.seq.rap.GenomeCommandLineProgram
coordinateSpacebroad.pda.seq.rap.GenomeCommandLineProgramprotected
customCommandLineValidation()broad.pda.seq.rap.GenomeCommandLineProgramprotected
doWork()broad.pda.seq.rap.ShuffleBAMprotected
GENEbroad.pda.seq.rap.GenomeCommandLineProgram
getCoordinateSpace()broad.pda.seq.rap.GenomeCommandLineProgramprotected
getGenes()broad.pda.seq.rap.GenomeCommandLineProgram
getRegions()broad.pda.seq.rap.GenomeCommandLineProgram
getRegionSet()broad.pda.seq.rap.GenomeCommandLineProgram
getRegionsMap()broad.pda.seq.rap.GenomeCommandLineProgram
INPUTbroad.pda.seq.rap.ShuffleBAM
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.GenomeCommandLineProgramprotected
main(final String[] args)broad.pda.seq.rap.ShuffleBAMstatic
MASK_FILEbroad.pda.seq.rap.GenomeCommandLineProgram
MAX_FRAGMENT_LENGTHbroad.pda.seq.rap.GenomeCommandLineProgram
MIN_MAPPING_QUALITYbroad.pda.seq.rap.GenomeCommandLineProgram
OUTPUTbroad.pda.seq.rap.ShuffleBAM
PCT_MASKED_ALLOWEDbroad.pda.seq.rap.GenomeCommandLineProgram
PERMUTATIONSbroad.pda.seq.rap.ShuffleBAM
RANDOM_SEEDbroad.pda.seq.rap.ShuffleBAM
REGIONbroad.pda.seq.rap.GenomeCommandLineProgram
SIZESbroad.pda.seq.rap.GenomeCommandLineProgram
USAGEbroad.pda.seq.rap.ShuffleBAM
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