Here is a list of all class members with links to the classes they belong to:

- u -

• uminus() : Jama.Matrix
• UnableToFitException() : broad.core.siphy.UnableToFitException
• unchunk() : broad.core.sequence.FastaSequenceIO
• UnfairDie() : broad.core.math.UnfairDie
• UNGAPPED_ALPHABET_SIZE : broad.core.multiplealignment.MultipleAlignment
• ungappedMatchStartOnFirstSequence() : umms.core.alignment.SmithWatermanAlignment
• union() : broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval , umms.core.annotation.SingleInterval
• UNKNOWN : umms.core.annotation.Annotation.Strand
• unloadAllSequences() : broad.core.sequence.Sequence
• unloadEncodedSequence() : broad.core.sequence.Sequence
• unloadSequence() : broad.core.sequence.Sequence , broad.pda.feature.genome.Chromosome
• UnorderedGenePair() : umms.core.alignment.FeatureSequenceAlignment.UnorderedGenePair
• unsetStranded() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• UP : jaligner.Directions
• updateBoundariesWithoutCrossingIntrons() : broad.core.util.CollapseByIntersection
• updateDistanceToNeighbors() : broad.pda.gene.NeighborAnalysis
• updateGeneByFirstCounts() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• updateIsoformsNameWithLocusName() : broad.pda.annotation.Locus
• updateReadInfoWithBarcode() : broad.pda.seq.fastq.FastqSplitterByBarcode
• updateScores() : umms.core.model.score.MultiScore
• updateScrToBedScore() : broad.pda.annotation.BEDFileParser , broad.pda.gene.GeneWithIsoforms
• uploadSetOfFiles() : broad.pda.annotation.BEDFileParser
• uppercase() : broad.core.sequence.Sequence
• 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
• useMergedUn() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly