- u -

• uminus() : Jama.Matrix
• UnableToFitException() : broad.core.siphy.UnableToFitException
• unchunk() : broad.core.sequence.FastaSequenceIO
• UnfairDie() : broad.core.math.UnfairDie
• 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
• 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
• 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
• useMergedUn() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly