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

- l -

• l2a() : umms.core.scripture.BuildScriptureCoordinateSpace
• lastIdxWhereListSearchBroke() : broad.core.annotation.BasicGenomicAnnotation
• LEFT : jaligner.Directions
• leftIntersect() : broad.core.math.EmpiricalDistribution
• length() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment , broad.core.sequence.SequenceRegion , broad.pda.datastructures.Alignments , broad.pda.feature.genome.Chromosome , jaligner.Sequence , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval
• LengthScore() : umms.core.model.score.LengthScore
• LINE_LENGTH : broad.core.sequence.FastaSequenceIO
• listFromArray() : broad.core.util.CLUtil
• load() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.annotation.BasicGenomicAnnotationReader , broad.core.annotation.BEDGraphReader , broad.core.annotation.BEDReader , broad.core.annotation.RepeatMaskerAnnotationReader , broad.core.annotation.ShortBEDReader , broad.core.motif.PositionWeightMatrixIO , broad.core.multiplealignment.FastaMultipleAlignmentIO , broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MAFIO , broad.core.multiplealignment.MultipleAlignmentIO , broad.core.multiplealignment.PhylipInterleavedMultipleAlignmentIO , broad.core.multiplealignment.PhylipSequencialMultipleAlignmentIO , broad.core.siphy.StationaryDistributionIO , broad.core.siphy.TreeScalerIO , broad.pda.datastructures.AlignmentsReader , broad.pda.seq.alignment.StoredAlignmentStats , umms.core.annotation.AnnotationFileReader
• loadAlignmentData() : broad.pda.annotation.BEDFileParser , broad.pda.seq.alignment.AlignmentUtils
• loadAlignmentDataByChr() : broad.pda.annotation.BEDFileParser
• loadAlignmentDataByChr3Prime() : broad.pda.annotation.BEDFileParser
• loadAlignmentDataByChr5Prime() : broad.pda.annotation.BEDFileParser
• loadAlignmentDataByChrArrayList() : broad.pda.annotation.BEDFileParser
• loadAlignmentDataToTree() : broad.pda.annotation.BEDFileParser
• loadAlignmentModel() : broad.pda.seq.rap.GenomeCommandLineProgram , broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
• loadAll() : broad.core.sequence.FastaSequenceIO
• loadAnnotations() : umms.core.utils.AnnotationUtils
• loadAtMostRandom() : broad.core.siphy.TreeScalerIO
• loadChrSizes() : broad.pda.annotation.BEDFileParser
• loadCoordinateSpace() : broad.pda.seq.rap.GenomeCommandLineProgram , broad.pda.seq.rap.PlotAggregateRegions , broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
• loadData() : broad.core.util.ParseGCTFile , broad.pda.annotation.BEDFileParser
• loadDataByChr() : broad.pda.annotation.BEDFileParser
• loadDataByChrToTree() : broad.pda.annotation.BEDFileParser
• loadDataByName() : broad.pda.annotation.BEDFileParser
• loadDataLine() : broad.pda.annotation.BEDFileParser
• loadedPairsAsFragments() : broad.pda.seq.segmentation.GenericAlignmentDataModel
• loadFromAscii() : broad.core.sequence.FastaQualityIndex
• loadGoMap() : broad.pda.gene.functionalAnnotation
• loadGTF() : broad.pda.annotation.BEDFileParser
• loadIndex() : broad.core.multiplealignment.MAFAlignment
• loadIntegrated() : broad.core.siphy.TreeScalerIO
• loadIntoDistribution() : broad.core.siphy.StationaryDistributionIO , broad.core.siphy.TreeScalerIO
• loadIsoformDataByChrToTree() : broad.pda.annotation.BEDFileParser , broad.pda.annotation.GTFFileParser
• loadList() : broad.pda.annotation.BEDFileParser
• loadOldIntegrated() : broad.core.siphy.TreeScalerIO
• loadPIDName() : broad.core.util.ParseGCTFile
• loadRNAAlignmentModel() : broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
• loadSequence() : broad.pda.feature.genome.Chromosome
• loadSequences() : broad.core.sequence.FastaSequenceIO
• loadSequencesByNameFromDirectory() : broad.core.sequence.FastaSequenceIO
• LocationAwareMatrix() : broad.pda.datastructures.LocationAwareMatrix
• Locus() : broad.pda.annotation.Locus
• Loess() : broad.core.math.Loess
• log10() : broad.core.datastructures.MatrixWithHeaders
• log2() : broad.core.datastructures.MatrixWithHeaders , broad.core.math.Loess , broad.core.math.MathUtil , broad.core.util.CLUtil
• logger : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.MultiSampleScanPeakCaller , broad.pda.seq.protection.SampleData , broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller , broad.pda.seq.protection.WindowScores , broad.pda.seq.rap.RAPPeakCaller , umms.core.utils.AnnotationUtils
• logTransform() : broad.core.util.ParseGCTFile
• LONG_READ_FLOW : broad.core.sequence.Sequence
• lu() : Jama.Matrix
• LUDecomposition() : Jama.LUDecomposition