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

- o -

• offset : broad.core.sequence.AbstractFastaParser
• 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
• ORIGINAL_ARRAY_LEFT : broad.pda.seq.rap.CountProbes
• ORIGINAL_ARRAY_RIGHT : broad.pda.seq.rap.CountProbes
• OUTER_LENGTH : broad.pda.seq.rap.PlotAggregateRegions
• outOrientedDegree() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• OUTPUT : broad.pda.samtools.FilterPairedReadsByMAQ , broad.pda.samtools.PairedEndTDF , broad.pda.samtools.TrimFastqReads , broad.pda.seq.rap.BuildRatioNullDistribution , broad.pda.seq.rap.CalculateCoverageStats , broad.pda.seq.rap.CollectAnnotationEnrichments , broad.pda.seq.rap.CountProbes , broad.pda.seq.rap.CountReads , broad.pda.seq.rap.DistanceToBED , broad.pda.seq.rap.GCContent , broad.pda.seq.rap.PlotAggregateRegions , broad.pda.seq.rap.RatioPermutationPeakCaller , 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
• OUTPUT_1 : broad.pda.samtools.FilterFastqReads
• OUTPUT_2 : broad.pda.samtools.FilterFastqReads
• overlap() : broad.pda.gene.GeneTools
• OVERLAP : broad.pda.seq.rap.BuildRatioNullDistribution , broad.pda.seq.rap.CountProbes , broad.pda.seq.rap.PlotAggregateRegions , broad.pda.seq.rap.RatioPermutationPeakCaller , broad.pda.seq.rap.SkellamKLPeakCaller , broad.pda.seq.rap.SlideAndCalculate , broad.pda.seq.rap.SlideAndCount
• 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