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• omegaEMIteration() : broad.core.siphy.EvolutionaryModel
• or() : umms.core.general.Predicates
• orientationForGene() : broad.pda.gene.GeneTools
• orientationFromSpliceSites() : broad.pda.gene.GeneTools
• OrientedChromosomeTranscriptGraph() : umms.core.scripture.OrientedChromosomeTranscriptGraph
• outOrientedDegree() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• overlap() : broad.pda.gene.GeneTools
• overlap_GenomicLevel() : broad.pda.annotation.BEDFileParser
• overlapByGenomicRegion() : broad.pda.annotation.BEDFileParser
• OverlapFilter() : umms.core.annotation.filter.OverlapFilter
• OverlapIterator() : broad.core.datastructures.IntervalTree< V >.OverlapIterator
• overlappers() : broad.core.datastructures.IntervalTree< V >
• overlappingValueIterator() : broad.core.datastructures.IntervalTree< V >
• overlaps() : broad.core.annotation.BasicLightweightAnnotation , broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment , broad.core.sequence.SequenceRegion , broad.pda.gene.GeneWithIsoforms , broad.pda.seq.graph.Path , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval , umms.core.annotation.Gene , umms.core.annotation.SingleInterval
• overlaps2() : umms.core.annotation.Gene
• overlapsAtAll() : broad.pda.datastructures.Alignments
• overlapsByGenomicRegion() : broad.pda.gene.GeneWithIsoforms
• overlapsCollection() : broad.pda.datastructures.Alignments
• overlapsExon() : broad.pda.gene.GeneWithIsoforms , umms.core.annotation.Gene
• overlapsGene() : umms.core.annotation.Gene
• overlapsGeneInAnyOrientation() : umms.core.annotation.Gene
• overlapsLeft() : broad.pda.seq.graph.Path
• overlapsRight() : broad.pda.seq.graph.Path
• overlapsStranded() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.Gene