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• A_CODE : broad.core.multiplealignment.MultipleAlignment
• AcuI : broad.core.primer3.RestrictionEnzyme
• allNucleotides : broad.core.sequence.TranscribedSequenceComposition
• allSamples : broad.pda.seq.protection.MultiSampleScanPeakCaller
• ANALYSIS_NAME : broad.pda.seq.rap.CollectAnnotationEnrichments
• ANNOTATION : broad.pda.seq.rap.GenomeCommandLineProgram
• annotation : umms.core.model.score.WindowScore.AbstractWindowScore
• ANNOTATION_BASE : broad.pda.seq.rap.CollectAnnotationEnrichments
• ANNOTATION_FILE : broad.pda.seq.rap.CountReads , broad.pda.seq.rap.PlotAggregateRegions , broad.pda.seq.rap.rna.CountReads
• ANNOTATIONS : broad.pda.seq.rap.CollectAnnotationEnrichments
• annotations : umms.core.annotation.AnnotationList< T extends Annotation >
• ARRAY_140105 : broad.pda.seq.rap.CountProbes