# 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.flow,
- 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.concurrent.AbstractExecutorService (implements java.util.concurrent.ExecutorService)
    - java.util.concurrent.ThreadPoolExecutor
      - picard.util.ThreadPoolExecutorWithExceptions
  - 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
  - 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
    - java.util.TreeMap<K,V> (implements java.lang.Cloneable, java.util.NavigableMap<K,V>, java.io.Serializable)
      - picard.fingerprint.Fingerprint
      - picard.pedigree.PedFile
  - picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
  - picard.analysis.AbstractWgsMetricsCollector<T>
    - picard.analysis.CollectWgsMetrics.WgsMetricsCollector
      - picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
    - 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.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.CollectQualityYieldMetricsFlow.QualityYieldMetricsCollectorFlow
  - picard.analysis.CollectQualityYieldMetricsSNVQ.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.MarkDuplicatesWithMateCigar
      - picard.sam.markduplicates.EstimateLibraryComplexity
    - picard.util.AccumulateQualityYieldMetrics
    - picard.vcf.AccumulateVariantCallingMetrics
    - picard.sam.AddCommentsToBam
    - picard.sam.AddOATag
    - picard.sam.AddOrReplaceReadGroups
    - picard.util.BaitDesigner
    - picard.sam.BamIndexStats
    - 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.analysis.CollectUmiPrevalenceMetrics
    - 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.CollectQualityYieldMetricsFlow
      - picard.analysis.CollectQualityYieldMetricsSNVQ
      - 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.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.CountingFilterWrapper
    - 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.flow.FlowBasedArgumentCollection (implements java.io.Serializable)
  - picard.flow.FlowBasedKeyCodec
  - picard.flow.FlowBasedRead
  - picard.flow.FlowReadGroupInfo
  - picard.nio.GATKUtils
  - 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.NamedFeature)
    - picard.annotation.Gene (implements java.lang.Iterable<T>)
  - 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.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.analysis.CompareMetrics.MetricComparisonDifferences
    - 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.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
      - picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
      - picard.analysis.CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow
      - picard.analysis.CollectQualityYieldMetricsSNVQ.QualityYieldMetrics
      - picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
        - picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
      - picard.sam.DuplicationMetrics
        - picard.sam.FlowBasedDuplicationMetrics
      - picard.sam.SamErrorMetric.ErrorMetric
        - picard.sam.SamErrorMetric.BaseErrorMetric
          - picard.sam.SamErrorMetric.IndelErrorMetric
        - picard.sam.SamErrorMetric.OverlappingErrorMetric
      - 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.nio.PicardBucketUtils
  - picard.cmdline.PicardCommandLine
  - picard.nio.PicardIOUtils
  - 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.SeriesStats
  - picard.util.SingleBarcodeDistanceMetric
  - picard.fingerprint.Snp (implements java.lang.Comparable<T>, htsjdk.samtools.util.Locatable)
  - 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.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)

## 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>
- 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 Interface 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 Class Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, 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.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection.FLOW_DUPLICATE_SELECTION_STRATEGY
    - 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