- r -

• random : broad.pda.seq.protection.MultiSampleScanPeakCaller
• RANDOM_SEED : broad.pda.seq.rap.BuildRatioNullDistribution , broad.pda.seq.rap.ShuffleBAM
• READ_LIST_FILE : broad.pda.samtools.FilterFastqReads
• readCigarFlag : umms.core.writers.PairedEndWriter
• readStartFlag : umms.core.writers.PairedEndWriter
• REF : broad.pda.seq.rap.DistanceToBED
• REFERENCE_SEQUENCE : broad.pda.seq.rap.GCContent
• REG_PATTERN : broad.core.annotation.BasicGenomicAnnotationReader
• REGION : broad.pda.seq.rap.GenomeCommandLineProgram
• region : umms.core.coordinatesystem.ShuffledIterator< T extends Annotation >
• REMOVE_MATE : broad.pda.samtools.FilterPairedReadsByMAQ
• removeAtEnd : broad.pda.samtools.TrimFastqReads
• removeAtStart : broad.pda.samtools.TrimFastqReads
• repeatMaskerAnnotationFactory : broad.core.annotation.AnnotationFactoryFactory
• RIGHT_MARGIN : broad.core.annotation.BasicGenomicAnnotationReader
• RPKM_OFFSET : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• RPKM_RATIO_OFFSET : broad.pda.seq.rap.SlideAndCalculate