Hierarchy For All Packages
Package Hierarchies:- picard,
- picard.analysis,
- picard.analysis.artifacts,
- picard.analysis.directed,
- picard.analysis.replicates,
- picard.annotation,
- picard.arrays,
- picard.arrays.illumina,
- picard.cmdline,
- picard.cmdline.argumentcollections,
- picard.cmdline.programgroups,
- picard.fastq,
- picard.filter,
- picard.fingerprint,
- picard.illumina,
- picard.illumina.parser,
- picard.illumina.parser.fakers,
- picard.illumina.parser.readers,
- picard.illumina.quality,
- picard.metrics,
- picard.nio,
- picard.pedigree,
- picard.reference,
- picard.sam,
- picard.sam.markduplicates,
- picard.sam.markduplicates.util,
- picard.sam.SamErrorMetric,
- picard.sam.util,
- picard.util,
- picard.util.help,
- picard.util.IntervalList,
- picard.vcf,
- picard.vcf.filter,
- picard.vcf.MendelianViolations,
- picard.vcf.processor,
- picard.vcf.processor.util
Class Hierarchy
- java.lang.Object
- picard.sam.AbstractAlignmentMerger
- picard.sam.SamAlignmentMerger
- java.util.AbstractCollection<E> (implements java.util.Collection<E>)
- java.util.AbstractSet<E> (implements java.util.Set<E>)
- java.util.TreeSet<E> (implements java.lang.Cloneable, java.util.NavigableSet<E>, java.io.Serializable)
- picard.fingerprint.FingerprintUtils.VariantContextSet
- java.util.TreeSet<E> (implements java.lang.Cloneable, java.util.NavigableSet<E>, java.io.Serializable)
- java.util.AbstractSet<E> (implements java.util.Set<E>)
- java.util.concurrent.AbstractExecutorService (implements java.util.concurrent.ExecutorService)
- java.util.concurrent.ThreadPoolExecutor
- picard.util.ThreadPoolExecutorWithExceptions
- java.util.concurrent.ThreadPoolExecutor
- picard.illumina.parser.readers.AbstractIlluminaPositionFileReader (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.illumina.parser.readers.ClocsFileReader
- picard.illumina.parser.readers.LocsFileReader
- picard.illumina.parser.readers.PosFileReader
- picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
- htsjdk.samtools.util.AbstractIterator<E> (implements java.util.Iterator<E>)
- picard.util.AbstractInputParser (implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
- picard.util.BasicInputParser
- picard.util.CsvInputParser
- picard.util.TabbedInputParser
- picard.util.BasicInputParser
- picard.util.AbstractInputParser (implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
- java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
- java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
- htsjdk.samtools.util.CollectionUtil.DefaultingMap<K,V>
- picard.vcf.MendelianViolations.MendelianViolationsByFamily
- htsjdk.samtools.util.CollectionUtil.DefaultingMap<K,V>
- java.util.TreeMap<K,V> (implements java.lang.Cloneable, java.util.NavigableMap<K,V>, java.io.Serializable)
- picard.fingerprint.Fingerprint
- picard.pedigree.PedFile
- java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
- picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
- picard.analysis.AbstractWgsMetricsCollector<T>
- picard.analysis.CollectWgsMetrics.WgsMetricsCollector
- picard.analysis.FastWgsMetricsCollector
- picard.util.AdapterMarker
- picard.analysis.AdapterUtility
- picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- picard.vcf.filter.AlleleBalanceFilter (implements picard.vcf.filter.VariantFilter)
- picard.util.AlleleSubsettingUtils
- picard.arrays.illumina.ArraysControlInfo
- picard.util.AsyncIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.util.BarcodeEditDistanceQuery
- picard.illumina.BarcodeExtractor
- picard.illumina.BarcodeExtractor.BarcodeMatch
- picard.illumina.parser.readers.BarcodeFileReader (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.illumina.parser.readers.BaseBclReader
- picard.illumina.parser.readers.BclReader (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.illumina.parser.readers.CbclReader (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.illumina.parser.readers.BaseBclReader.CycleData
- picard.illumina.parser.readers.BaseBclReader.TileData
- picard.cmdline.programgroups.BaseCallingProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.illumina.BasecallsConverter<CLUSTER_OUTPUT_RECORD>
- picard.illumina.SortedBasecallsConverter<CLUSTER_OUTPUT_RECORD>
- picard.illumina.UnsortedBasecallsConverter<CLUSTER_OUTPUT_RECORD>
- picard.illumina.BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD>
- picard.sam.SamErrorMetric.BaseErrorAggregation<CALCULATOR>
- picard.sam.SamErrorMetric.BaseErrorCalculator (implements picard.sam.SamErrorMetric.BaseCalculator)
- picard.sam.SamErrorMetric.IndelErrorCalculator
- picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
- picard.sam.SamErrorMetric.SimpleErrorCalculator
- picard.illumina.parser.BaseIlluminaDataProvider (implements java.lang.AutoCloseable, java.lang.Iterable<T>, java.util.Iterator<E>)
- picard.illumina.parser.BclData
- picard.illumina.parser.CbclData
- picard.illumina.parser.readers.BclIndexReader
- picard.illumina.parser.readers.BclQualityEvaluationStrategy
- picard.sam.BestEndMapqPrimaryAlignmentStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- picard.sam.BestMapqPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- picard.vcf.ByIntervalListVariantContextIterator (implements java.util.Iterator<E>)
- picard.vcf.CallingMetricAccumulator (implements picard.vcf.processor.VariantProcessor.Accumulator<RESULT>)
- picard.vcf.GvcfMetricAccumulator
- picard.vcf.CallingMetricAccumulator.Result
- picard.fastq.Casava18ReadNameEncoder (implements picard.fastq.ReadNameEncoder)
- picard.analysis.ChimeraUtil
- picard.util.CircularByteBuffer
- picard.cmdline.ClassFinder
- picard.util.ClippingUtility
- picard.illumina.parser.ClusterData
- picard.illumina.ClusterDataToSamConverter (implements picard.illumina.BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD>)
- picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier
- picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
- picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection (implements picard.cmdline.argumentcollections.IntervalArgumentCollection)
- picard.cmdline.CommandLineDefaults
- picard.cmdline.CommandLineProgram
- picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- picard.sam.markduplicates.MarkDuplicates (implements picard.sam.markduplicates.MarkDuplicatesHelper)
- picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
- picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
- picard.sam.markduplicates.MarkDuplicatesWithMateCigar
- picard.sam.markduplicates.MarkDuplicates (implements picard.sam.markduplicates.MarkDuplicatesHelper)
- picard.sam.markduplicates.EstimateLibraryComplexity
- picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- picard.util.AccumulateQualityYieldMetrics
- picard.vcf.AccumulateVariantCallingMetrics
- picard.sam.AddCommentsToBam
- picard.sam.AddOATag
- picard.sam.AddOrReplaceReadGroups
- picard.util.BaitDesigner
- picard.sam.BamIndexStats
- picard.fastq.BamToBfq
- picard.util.BedToIntervalList
- picard.arrays.illumina.BpmToNormalizationManifestCsv
- picard.sam.BuildBamIndex
- picard.fingerprint.CalculateFingerprintMetrics
- picard.sam.CalculateReadGroupChecksum
- picard.sam.markduplicates.CheckDuplicateMarking
- picard.fingerprint.CheckFingerprint
- picard.illumina.CheckIlluminaDirectory
- picard.sam.CheckTerminatorBlock
- picard.sam.CleanSam
- picard.fingerprint.ClusterCrosscheckMetrics
- picard.arrays.CollectArraysVariantCallingMetrics
- picard.illumina.quality.CollectHiSeqXPfFailMetrics
- picard.illumina.CollectIlluminaBasecallingMetrics
- picard.illumina.CollectIlluminaLaneMetrics
- picard.analysis.replicates.CollectIndependentReplicateMetrics
- picard.analysis.CollectJumpingLibraryMetrics
- picard.analysis.CollectMultipleMetrics
- picard.analysis.CollectOxoGMetrics
- picard.analysis.CollectRrbsMetrics
- picard.sam.SamErrorMetric.CollectSamErrorMetrics
- picard.analysis.directed.CollectTargetedMetrics<METRIC,COLLECTOR>
- picard.analysis.directed.CollectHsMetrics
- picard.analysis.directed.CollectTargetedPcrMetrics
- picard.vcf.CollectVariantCallingMetrics
- picard.analysis.CollectWgsMetrics
- picard.analysis.CollectRawWgsMetrics
- picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- picard.arrays.CombineGenotypingArrayVcfs
- picard.arrays.illumina.CompareGtcFiles
- picard.analysis.CompareMetrics
- picard.sam.CompareSAMs
- picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- picard.arrays.CreateBafRegressMetricsFile
- picard.arrays.illumina.CreateExtendedIlluminaManifest
- picard.sam.CreateSequenceDictionary
- picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- picard.fingerprint.CrosscheckFingerprints
- picard.fingerprint.CrosscheckReadGroupFingerprints
- picard.sam.DownsampleSam
- picard.illumina.ExtractBarcodesProgram
- picard.illumina.ExtractIlluminaBarcodes
- picard.illumina.IlluminaBasecallsToFastq
- picard.illumina.IlluminaBasecallsToSam
- picard.fingerprint.ExtractFingerprint
- picard.reference.ExtractSequences
- picard.sam.FastqToSam
- picard.util.FifoBuffer
- picard.sam.FilterSamReads
- picard.vcf.filter.FilterVcf
- picard.vcf.MendelianViolations.FindMendelianViolations
- picard.sam.FixMateInformation
- picard.vcf.FixVcfHeader
- picard.sam.GatherBamFiles
- picard.vcf.GatherVcfs
- picard.vcf.GenotypeConcordance
- picard.arrays.GtcToVcf
- picard.fingerprint.IdentifyContaminant
- picard.util.IntervalListToBed
- picard.util.IntervalListTools
- picard.fingerprint.LiftOverHaplotypeMap
- picard.util.LiftOverIntervalList
- picard.vcf.LiftoverVcf
- picard.vcf.MakeSitesOnlyVcf
- picard.vcf.MakeVcfSampleNameMap
- picard.illumina.MarkIlluminaAdapters
- picard.sam.MergeBamAlignment
- picard.arrays.MergePedIntoVcf
- picard.sam.MergeSamFiles
- picard.vcf.MergeVcfs
- picard.reference.NonNFastaSize
- picard.reference.NormalizeFasta
- picard.sam.PositionBasedDownsampleSam
- picard.vcf.RenameSampleInVcf
- picard.sam.ReorderSam
- picard.sam.ReplaceSamHeader
- picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- picard.sam.RevertSam
- picard.sam.SamFormatConverter
- picard.sam.SamToFastq
- picard.sam.SamToFastqWithTags
- picard.util.ScatterIntervalsByNs
- picard.sam.SetNmMdAndUqTags
- picard.sam.SetNmAndUqTags
- picard.analysis.SinglePassSamProgram
- picard.analysis.CollectAlignmentSummaryMetrics
- picard.analysis.CollectBaseDistributionByCycle
- picard.sam.markduplicates.CollectDuplicateMetrics
- picard.analysis.CollectGcBiasMetrics
- picard.analysis.CollectInsertSizeMetrics
- picard.analysis.CollectQualityYieldMetrics
- picard.analysis.CollectRnaSeqMetrics
- picard.analysis.artifacts.CollectSequencingArtifactMetrics
- picard.analysis.MeanQualityByCycle
- picard.analysis.QualityScoreDistribution
- picard.annotation.SortGff
- picard.sam.SortSam
- picard.vcf.SortVcf
- picard.sam.SplitSamByLibrary
- picard.sam.SplitSamByNumberOfReads
- picard.vcf.SplitVcfs
- picard.vcf.UpdateVcfSequenceDictionary
- picard.sam.ValidateSamFile
- picard.vcf.VcfFormatConverter
- picard.arrays.VcfToAdpc
- picard.vcf.VcfToIntervalList
- picard.sam.ViewSam
- picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- picard.cmdline.CommandLineSyntaxTranslater
- picard.analysis.CounterManager
- picard.analysis.CounterManager.Counter
- picard.filter.CountingFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- picard.filter.CountingAdapterFilter
- picard.filter.CountingDuplicateFilter
- picard.filter.CountingMapQFilter
- picard.filter.CountingPairedFilter
- picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- picard.util.DbSnpBitSetUtil
- picard.util.DbSnpBitSetUtil.DbSnpBitSets
- picard.util.DelimitedTextFileWithHeaderIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.util.DelimitedTextFileWithHeaderIterator.Row
- picard.vcf.filter.DepthFilter (implements picard.vcf.filter.GenotypeFilter)
- picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap (implements picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap)
- picard.sam.DuplicationMetricsFactory
- picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader (implements java.util.Iterator<E>)
- picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- picard.cmdline.argumentcollections.EmptyOutputArgumentCollection (implements picard.cmdline.argumentcollections.OutputArgumentCollection)
- picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor (implements java.lang.Runnable)
- picard.illumina.parser.fakers.FileFaker
- picard.illumina.parser.fakers.BarcodeFileFaker
- picard.illumina.parser.fakers.BciFileFaker
- picard.illumina.parser.fakers.BclFileFaker
- picard.illumina.parser.fakers.BclIndexFaker
- picard.illumina.parser.fakers.ClocsFileFaker
- picard.illumina.parser.fakers.FilterFileFaker
- picard.illumina.parser.fakers.LocsFileFaker
- picard.illumina.parser.fakers.MultiTileBclFileFaker
- picard.illumina.parser.fakers.MultiTileLocsFileFaker
- picard.illumina.parser.fakers.PosFileFaker
- picard.vcf.filter.FilterApplyingVariantIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.illumina.parser.readers.FilterFileReader (implements java.util.Iterator<E>)
- picard.fingerprint.FingerprintChecker
- picard.fingerprint.FingerprintIdDetails
- picard.fingerprint.FingerprintResults
- picard.fingerprint.FingerprintUtils
- picard.vcf.filter.FisherStrandFilter (implements picard.vcf.filter.VariantFilter)
- picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- picard.analysis.GcBiasUtils
- picard.annotation.Gene.Transcript
- picard.annotation.Gene.Transcript.Exon
- picard.annotation.GeneAnnotationReader
- picard.vcf.GenotypeConcordance.Alleles
- picard.vcf.GenotypeConcordanceCounts
- picard.vcf.GenotypeConcordanceScheme
- picard.vcf.GA4GHScheme
- picard.vcf.GA4GHSchemeWithMissingAsHomRef
- picard.vcf.GenotypeConcordanceSchemeFactory
- picard.vcf.GenotypeConcordanceStates
- picard.vcf.GenotypeConcordanceStates.TruthAndCallStates (implements java.lang.Comparable<T>)
- picard.vcf.filter.GenotypeQualityFilter (implements picard.vcf.filter.GenotypeFilter)
- picard.cmdline.programgroups.GenotypingArraysProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.util.GraphUtils
- picard.util.GraphUtils.Graph<Node>
- picard.fingerprint.HaplotypeBlock (implements java.lang.Comparable<T>)
- picard.fingerprint.HaplotypeMap
- picard.fingerprint.HaplotypeProbabilities
- picard.fingerprint.CappedHaplotypeProbabilities
- picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
- picard.fingerprint.HaplotypeProbabilitiesFromSequence
- picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- picard.util.help.HelpConstants
- htsjdk.io.HtsPath (implements htsjdk.io.IOPath, java.io.Serializable)
- picard.nio.PicardHtsPath
- picard.arrays.illumina.IlluminaAdpcFileWriter (implements java.lang.AutoCloseable)
- picard.arrays.illumina.IlluminaAdpcFileWriter.Record
- picard.arrays.illumina.IlluminaBPMLocusEntry
- picard.illumina.parser.IlluminaDataProviderFactory
- picard.illumina.parser.IlluminaFileUtil
- picard.arrays.illumina.IlluminaManifest
- picard.arrays.illumina.Build37ExtendedIlluminaManifest
- picard.arrays.illumina.IlluminaManifestRecord
- picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- picard.fastq.IlluminaReadNameEncoder (implements picard.fastq.ReadNameEncoder)
- picard.util.IlluminaUtil
- picard.arrays.illumina.InfiniumDataFile
- picard.arrays.illumina.IlluminaBPMFile (implements java.lang.AutoCloseable)
- picard.arrays.illumina.InfiniumEGTFile (implements java.lang.AutoCloseable)
- picard.arrays.illumina.InfiniumGTCFile (implements java.lang.AutoCloseable)
- picard.arrays.illumina.InfiniumFileTOC
- picard.arrays.illumina.InfiniumGTCRecord
- picard.arrays.illumina.InfiniumNormalizationManifest
- picard.arrays.illumina.InfiniumTransformation
- picard.arrays.illumina.InfiniumVcfFields
- picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- htsjdk.samtools.util.Interval (implements java.lang.Cloneable, java.lang.Comparable<T>, htsjdk.tribble.Feature)
- picard.util.IntervalList.IntervalListScatter (implements java.lang.Iterable<T>)
- picard.util.IntervalList.IntervalListScattererByBaseCount (implements picard.util.IntervalList.IntervalListScatterer)
- picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- picard.util.IntervalList.IntervalListScattererWithoutSubdivisionWithOverflow
- picard.util.IntervalList.IntervalListScattererWithSubdivision
- picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- picard.util.IntervalList.IntervalListScattererByIntervalCount (implements picard.util.IntervalList.IntervalListScatterer)
- picard.util.IntervalList.IntervalListScattererByIntervalCountWithDistributedRemainder
- picard.cmdline.programgroups.IntervalsManipulationProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.util.Iterators
- picard.illumina.LanePhasingMetricsCollector
- picard.sam.markduplicates.util.LibraryIdGenerator
- picard.util.LiftoverUtils
- picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- picard.sam.markduplicates.MarkDuplicatesForFlowHelper (implements picard.sam.markduplicates.MarkDuplicatesHelper)
- picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator (implements htsjdk.samtools.SAMRecordIterator)
- picard.sam.markduplicates.util.MarkQueue
- picard.fingerprint.MatchResults (implements java.lang.Comparable<T>)
- picard.util.MathUtil
- picard.util.MathUtil.LogMath
- picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap (implements picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap)
- htsjdk.samtools.metrics.MetricBase
- picard.arrays.BafRegressMetrics
- picard.illumina.BarcodeMetric
- picard.analysis.BaseDistributionByCycleMetrics
- picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
- picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
- picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
- picard.analysis.CollectOxoGMetrics.CpcgMetrics
- picard.fingerprint.CrosscheckMetric
- picard.fingerprint.ClusteredCrosscheckMetric
- picard.analysis.FingerprintingDetailMetrics
- picard.analysis.FingerprintingSummaryMetrics
- picard.fingerprint.FingerprintMetrics
- picard.metrics.GcBiasMetrics
- picard.vcf.GenotypeConcordanceContingencyMetrics
- picard.vcf.GenotypeConcordanceDetailMetrics
- picard.vcf.GenotypeConcordanceSummaryMetrics
- picard.illumina.IlluminaBasecallingMetrics
- picard.illumina.IlluminaLaneMetrics
- picard.illumina.IlluminaPhasingMetrics
- picard.analysis.JumpingLibraryMetrics
- picard.analysis.MergeableMetricBase
- picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- picard.sam.DuplicationMetrics
- picard.sam.FlowBasedDuplicationMetrics
- picard.sam.SamErrorMetric.ErrorMetric
- picard.sam.SamErrorMetric.BaseErrorMetric
- picard.sam.SamErrorMetric.IndelErrorMetric
- picard.sam.SamErrorMetric.OverlappingErrorMetric
- picard.sam.SamErrorMetric.BaseErrorMetric
- picard.analysis.artifacts.ErrorSummaryMetrics
- picard.analysis.replicates.IndependentReplicateMetric
- picard.vcf.MendelianViolations.MendelianViolationMetrics
- picard.analysis.WgsMetrics
- picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
- picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
- picard.metrics.MultilevelMetrics
- picard.analysis.AlignmentSummaryMetrics
- picard.analysis.GcBiasDetailMetrics
- picard.analysis.GcBiasSummaryMetrics
- picard.analysis.InsertSizeMetrics
- picard.analysis.directed.PanelMetricsBase
- picard.analysis.directed.HsMetrics
- picard.analysis.directed.TargetMetricsBase
- picard.analysis.directed.TargetedPcrMetrics
- picard.analysis.directed.TargetMetrics
- picard.analysis.RnaSeqMetrics
- picard.analysis.RrbsCpgDetailMetrics
- picard.analysis.RrbsSummaryMetrics
- picard.sam.SamComparisonMetric
- picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
- picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
- picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
- picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
- picard.analysis.TheoreticalSensitivityMetrics
- picard.sam.markduplicates.UmiMetrics
- picard.arrays.VerifyIDIntensityContaminationMetrics
- picard.illumina.parser.readers.MMapBackedIteratorFactory
- picard.sam.MostDistantPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
- picard.metrics.MultiLevelCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE>
- picard.analysis.GcBiasMetricsCollector
- picard.analysis.directed.InsertSizeMetricsCollector
- picard.metrics.SAMRecordAndReferenceMultiLevelCollector<BEAN,HKEY>
- picard.analysis.AlignmentSummaryMetricsCollector
- picard.analysis.RrbsMetricsCollector
- picard.metrics.SAMRecordMultiLevelCollector<BEAN,HKEY>
- picard.analysis.directed.RnaSeqMetricsCollector
- picard.analysis.directed.TargetMetricsCollector<METRIC_TYPE>
- picard.analysis.directed.HsMetricCollector
- picard.analysis.directed.TargetedPcrMetricsCollector
- picard.illumina.parser.MultiTileBclParser
- picard.illumina.parser.MultiTileParser<OUTPUT_RECORD>
- picard.illumina.parser.MultiTileFilterParser
- picard.illumina.parser.MultiTileLocsParser
- picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- picard.cmdline.programgroups.OtherProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.illumina.parser.OutputMapping
- picard.sam.util.Pair<X,Y> (implements java.lang.Comparable<T>)
- picard.vcf.PairedVariantSubContextIterator (implements java.util.Iterator<E>)
- picard.vcf.PairedVariantSubContextIterator.VcfTuple
- picard.illumina.parser.ParameterizedFileUtil
- picard.illumina.parser.MultiTileBclFileUtil
- picard.illumina.parser.MultiTileFileUtil<OUTPUT_RECORD>
- picard.illumina.parser.PerTileFileUtil
- picard.illumina.parser.PerTileOrPerRunFileUtil
- picard.illumina.parser.PerTilePerCycleFileUtil
- picard.pedigree.PedFile.PedTrio
- picard.illumina.parser.PerTileParser<ILLUMINA_DATA>
- picard.illumina.parser.PosParser
- picard.sam.util.PGTagArgumentCollection
- picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
- picard.sam.util.PhysicalLocationInt (implements picard.sam.util.PhysicalLocation)
- picard.sam.util.PhysicalLocationShort
- picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- picard.sam.markduplicates.util.ReadEnds
- picard.sam.markduplicates.util.ReadEndsForMarkDuplicates (implements java.lang.Cloneable)
- picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- picard.sam.markduplicates.util.ReadEndsForMateCigar
- picard.sam.markduplicates.util.ReadEndsForMarkDuplicates (implements java.lang.Cloneable)
- picard.sam.util.PhysicalLocationShort
- picard.cmdline.PicardCommandLine
- picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
- picard.sam.util.PrimaryAlignmentKey (implements java.lang.Comparable<T>)
- picard.util.PropertyUtils
- picard.vcf.filter.QdFilter (implements picard.vcf.filter.VariantFilter)
- picard.util.QuerySortedReadPairIteratorUtil
- picard.util.QuerySortedReadPairIteratorUtil.ReadPair
- picard.illumina.parser.Range
- picard.sam.SamErrorMetric.ReadBaseStratification
- picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
- picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier<T,R> (implements picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>)
- picard.illumina.parser.ReadData
- picard.cmdline.programgroups.ReadDataManipulationProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.illumina.parser.ReadDescriptor
- picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
- picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
- picard.sam.util.ReadNameParser (implements java.io.Serializable)
- picard.sam.markduplicates.util.OpticalDuplicateFinder (implements java.io.Serializable)
- picard.illumina.parser.ReadStructure
- picard.illumina.parser.ReadStructure.Substructure (implements java.lang.Iterable<T>)
- picard.cmdline.programgroups.ReferenceProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.annotation.RefFlatReader
- picard.util.ReflectionUtil
- picard.sam.util.RepresentativeReadIndexer
- picard.sam.markduplicates.util.RepresentativeReadIndexerCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
- picard.cmdline.argumentcollections.RequiredOutputArgumentCollection (implements picard.cmdline.argumentcollections.OutputArgumentCollection)
- picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- picard.util.RExecutor
- picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- picard.sam.util.SamComparison
- picard.sam.util.SAMComparisonArgumentCollection
- picard.metrics.SAMRecordAndReference
- htsjdk.samtools.util.SamRecordWithOrdinal
- picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
- picard.fastq.SamToBfqWriter
- picard.fastq.BamToBfqWriter
- picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
- picard.util.SequenceDictionaryUtils
- picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator (implements java.util.Iterator<E>)
- picard.analysis.artifacts.SequencingArtifactMetrics
- picard.util.SingleBarcodeDistanceMetric
- picard.fingerprint.Snp (implements java.lang.Comparable<T>)
- picard.cmdline.StandardOptionDefinitions
- picard.util.TabbedTextFileWithHeaderParser (implements java.lang.AutoCloseable, java.lang.Iterable<T>)
- picard.util.TabbedTextFileWithHeaderParser.Row
- picard.analysis.directed.TargetMetricsCollector.Coverage
- picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
- picard.Test
- picard.cmdline.programgroups.Testing (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.analysis.TheoreticalSensitivity
- picard.analysis.TheoreticalSensitivity.RouletteWheel
- picard.util.ThreadPoolExecutorUtil
- java.lang.Throwable (implements java.io.Serializable)
- java.lang.Exception
- java.lang.RuntimeException
- picard.PicardException
- picard.annotation.AnnotationException
- picard.PicardException
- java.lang.RuntimeException
- java.lang.Exception
- picard.illumina.parser.Tile
- picard.illumina.parser.TileIndex (implements java.lang.Iterable<T>)
- picard.illumina.parser.TileIndex.TileIndexRecord
- picard.illumina.parser.readers.TileMetricsOutReader (implements java.util.Iterator<E>)
- picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- picard.illumina.parser.TileMetricsUtil
- picard.illumina.parser.TilePhasingValue
- picard.sam.markduplicates.UmiGraph
- picard.util.UnsignedTypeUtil
- picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased<A,R> (implements picard.vcf.processor.VariantAccumulatorExecutor<ACCUMULATOR,RESULT>)
- picard.cmdline.programgroups.VariantEvaluationProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.cmdline.programgroups.VariantFilteringProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.vcf.processor.VariantIteratorProducer
- picard.cmdline.programgroups.VariantManipulationProgramGroup (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
- picard.vcf.processor.VariantProcessor<RESULT,ACCUMULATOR>
- picard.vcf.processor.VariantProcessor.Builder<A,R>
- picard.vcf.processor.VcfFileSegment
- picard.vcf.processor.VcfFileSegmentGenerator
- picard.vcf.processor.VcfPathSegment
- picard.vcf.processor.VcfPathSegmentGenerator
- picard.vcf.VcfUtils
- picard.analysis.WgsMetricsProcessorImpl<T> (implements picard.analysis.WgsMetricsProcessor)
- picard.sam.AbstractAlignmentMerger
Interface Hierarchy
- picard.util.AdapterPair
- picard.util.AtomicIterator<T>
- java.lang.AutoCloseable
- java.io.Closeable
- htsjdk.io.Writer<A>
- picard.illumina.BasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD>
- htsjdk.io.Writer<A>
- java.io.Closeable
- picard.sam.SamErrorMetric.BaseCalculator
- picard.illumina.BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD>
- picard.analysis.CollectMultipleMetrics.ProgramInterface
- picard.vcf.filter.GenotypeFilter
- picard.cmdline.argumentcollections.IntervalArgumentCollection
- picard.util.IntervalList.IntervalListScatterer
- picard.sam.markduplicates.MarkDuplicatesHelper
- picard.cmdline.argumentcollections.OutputArgumentCollection
- picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>
- picard.sam.PrimaryAlignmentSelectionStrategy
- picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier<T>
- picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
- picard.fastq.ReadNameEncoder
- picard.cmdline.argumentcollections.ReferenceArgumentCollection
- java.io.Serializable
- picard.sam.util.PhysicalLocation
- picard.vcf.processor.VariantAccumulatorExecutor<ACCUMULATOR,RESULT>
- picard.vcf.filter.VariantFilter
- picard.vcf.processor.VariantProcessor.Accumulator<RESULT>
- picard.vcf.processor.VariantProcessor.AccumulatorGenerator<ACCUMULATOR,RESULT>
- picard.vcf.processor.VariantProcessor.ResultMerger<RESULT>
- picard.analysis.WgsMetricsProcessor
Annotation Type Hierarchy
- picard.analysis.MergeableMetricBase.MergeByAdding (implements java.lang.annotation.Annotation)
- picard.analysis.MergeableMetricBase.MergeByAssertEquals (implements java.lang.annotation.Annotation)
- picard.analysis.MergeableMetricBase.MergingIsManual (implements java.lang.annotation.Annotation)
- picard.analysis.MergeableMetricBase.NoMergingIsDerived (implements java.lang.annotation.Annotation)
- picard.analysis.MergeableMetricBase.NoMergingKeepsValue (implements java.lang.annotation.Annotation)
Enum Hierarchy
- java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
- picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- picard.analysis.AlignmentSummaryMetrics.Category
- picard.util.BaitDesigner.DesignStrategy
- picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
- picard.sam.markduplicates.CheckDuplicateMarking.Mode (implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
- picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
- picard.analysis.CollectMultipleMetrics.Program (implements picard.analysis.CollectMultipleMetrics.ProgramInterface, org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
- picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
- picard.fingerprint.CrosscheckMetric.DataType
- picard.fingerprint.CrosscheckMetric.FingerprintResult
- picard.fingerprint.DiploidGenotype
- picard.fingerprint.DiploidHaplotype
- picard.illumina.DistanceMetric (implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
- picard.sam.FilterSamReads.Filter (implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
- picard.vcf.GenotypeConcordanceStateCodes
- picard.vcf.GenotypeConcordanceStates.CallState
- picard.vcf.GenotypeConcordanceStates.ContingencyState
- picard.vcf.GenotypeConcordanceStates.TruthState
- picard.fingerprint.HaplotypeProbabilities.Genotype
- picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
- picard.illumina.parser.IlluminaDataType
- picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- picard.arrays.illumina.IlluminaGenotype
- picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- picard.illumina.parser.IlluminaMetricsCode
- picard.util.IlluminaUtil.IlluminaAdapterPair (implements picard.util.AdapterPair)
- picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
- picard.illumina.parser.IntensityChannel
- picard.util.IntervalList.IntervalListScatterMode (implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
- picard.util.IntervalListTools.Action (implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
- picard.annotation.LocusFunction
- picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
- picard.sam.markduplicates.MarkDuplicates.DuplicateType
- picard.analysis.MetricAccumulationLevel
- picard.nio.PathProvider
- picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
- picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
- picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
- picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
- picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
- picard.illumina.parser.ReadType
- picard.annotation.RefFlatReader.RefFlatColumns
- picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- picard.sam.RevertSam.FileType (implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
- picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
- picard.sam.util.SamComparison.AlignmentComparison
- picard.pedigree.Sex
- picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
- picard.illumina.parser.TileTemplateRead
- picard.analysis.artifacts.Transition
- picard.analysis.artifacts.Transition.Base
- picard.sam.ValidateSamFile.Mode
- picard.util.VariantType
- picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
- picard.sam.ViewSam.AlignmentStatus
- picard.sam.ViewSam.PfStatus
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)