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broad.pda.seq.rap.GenomeCommandLineProgram Member List

This is the complete list of members for broad.pda.seq.rap.GenomeCommandLineProgram, 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
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
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
MASK_FILEbroad.pda.seq.rap.GenomeCommandLineProgram
MAX_FRAGMENT_LENGTHbroad.pda.seq.rap.GenomeCommandLineProgram
MIN_MAPPING_QUALITYbroad.pda.seq.rap.GenomeCommandLineProgram
PCT_MASKED_ALLOWEDbroad.pda.seq.rap.GenomeCommandLineProgram
REGIONbroad.pda.seq.rap.GenomeCommandLineProgram
SIZESbroad.pda.seq.rap.GenomeCommandLineProgram
Generated on Fri Aug 15 2014 15:11:03 for ESAT by   doxygen 1.8.7