- u -

• UNGAPPED_ALPHABET_SIZE : broad.core.multiplealignment.MultipleAlignment
• UNKNOWN : umms.core.annotation.Annotation.Strand
• UP : jaligner.Directions
• USAGE : broad.core.annotation.AnnotationUtils , broad.core.math.EmpiricalDistribution , broad.core.math.Statistics , broad.core.motif.PositionWeightMatrixIO , broad.core.motif.PWMUtils , broad.core.motif.SequenceMotif , broad.core.motif.SequenceMotifCluster , broad.core.multiplealignment.AlignmentExtractor , broad.core.multiplealignment.MAFAlignment , broad.core.sequence.Extractor , broad.core.siphy.PiHMM , broad.core.siphy.TreeScaler , broad.pda.samtools.FilterFastqReads , broad.pda.samtools.PairedEndTDF , broad.pda.samtools.TrimFastqReads , broad.pda.seq.rap.BuildRatioNullDistribution , broad.pda.seq.rap.CollectAnnotationEnrichments , broad.pda.seq.rap.CountReads , broad.pda.seq.rap.GCContent , broad.pda.seq.rap.PlotAggregateRegions , broad.pda.seq.rap.RatioPermutationPeakCaller , broad.pda.seq.rap.rna.CollectRnaSeqMetrics , broad.pda.seq.rap.rna.CountReads , broad.pda.seq.rap.ShuffleBAM , broad.pda.seq.rap.ShuffleBED , broad.pda.seq.rap.SkellamKLPeakCaller , broad.pda.seq.rap.SlideAndCalculate , broad.pda.seq.rap.SlideAndCount , broad.pda.seq.rap.UnmarkDuplicates
• USE_INTERMEDIATES : broad.pda.seq.rap.BuildRatioNullDistribution