- d -

• data : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• DEFAULT_ALPHABET_SIZE : broad.core.motif.PositionWeightColumn
• DEFAULT_GAP_EXTEND_PENALTY : umms.core.alignment.FeatureSequenceAlignment , umms.core.alignment.SmithWatermanAlignment
• DEFAULT_GAP_OPEN_PENALTY : umms.core.alignment.FeatureSequenceAlignment , umms.core.alignment.SmithWatermanAlignment
• DEFAULT_INS_SIZE_PVAL : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• DEFAULT_INSERT_SIZE_FUDGE : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• DEFAULT_MAKE_GENE_OVERLAP : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• DEFAULT_MATCH_SCORE : umms.core.alignment.FeatureSequenceAlignment , umms.core.alignment.SmithWatermanAlignment
• DEFAULT_MIN_MAPPING_QUALITY : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• DEFAULT_MISMATCH_SCORE : umms.core.alignment.FeatureSequenceAlignment , umms.core.alignment.SmithWatermanAlignment
• DEFAULT_REGION_TOTAL : umms.core.model.score.CountScore , umms.core.model.score.PoissonEnrichmentScore
• DEFAULT_VALUE : umms.core.model.score.AbstractListScore
• degenerateCodonStarts : broad.core.multiplealignment.AlignmentExtractor
• DEPLETED : broad.pda.seq.rap.RatioPermutationPeakCaller , broad.pda.seq.rap.SkellamKLPeakCaller
• DIAGONAL : jaligner.Directions
• DISCRETE_EXTENSION : broad.pda.seq.rap.CollectAnnotationEnrichments