- c -

• C_CODE : broad.core.multiplealignment.MultipleAlignment
• CLIP_AT_BOUNDARIES : broad.pda.seq.rap.PlotAggregateRegions
• codonToAminoacid : broad.core.multiplealignment.AlignmentExtractor
• CONTINUOUS_EXTENSION : broad.pda.seq.rap.CollectAnnotationEnrichments
• CONTROL : broad.pda.seq.rap.BuildRatioNullDistribution , broad.pda.seq.rap.GenomeScoringProgram , broad.pda.seq.rap.RatioPermutationPeakCaller , broad.pda.seq.rap.rna.TranscriptomeScoringProgram
• controlSamples : broad.pda.seq.protection.MultiSampleScanPeakCaller
• COORD_SPACE : broad.pda.seq.rap.GenomeCommandLineProgram
• coordinateSpace : broad.pda.seq.rap.GenomeCommandLineProgram , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• cs : umms.core.coordinatesystem.ShuffledIterator< T extends Annotation >
• ctrl : broad.pda.seq.protection.WindowScores
• ctrlModel : umms.core.model.score.MultiScore
• currentBase : broad.core.sequence.AbstractFastaParser
• CUTOFF : broad.pda.seq.rap.RatioPermutationPeakCaller , broad.pda.seq.rap.SkellamKLPeakCaller