Hierarchy For All Packages

Package Hierarchies:

• picard,
• picard.analysis,
• picard.analysis.artifacts,
• picard.analysis.directed,
• picard.analysis.replicates,
• picard.annotation,
• 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.pedigree,
• picard.reference,
• picard.sam,
• picard.sam.markduplicates,
• picard.sam.markduplicates.util,
• picard.sam.util,
• picard.util,
• picard.util.help,
• 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.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.vcf.filter.AlleleBalanceFilter (implements picard.vcf.filter.VariantFilter)
  • picard.cmdline.programgroups.Alpha (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
  • picard.util.AsyncIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
  • picard.fastq.BamToBfqWriter
  • 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.illumina.parser.BaseIlluminaDataProvider (implements java.lang.AutoCloseable, java.lang.Iterable<T>, java.util.Iterator<E>)
    • picard.illumina.parser.IlluminaDataProvider
    • picard.illumina.parser.NewIlluminaDataProvider
  • 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.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
  • 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
          • picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
            • picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
        • picard.sam.markduplicates.MarkDuplicatesWithMateCigar
      • picard.sam.markduplicates.EstimateLibraryComplexity
    • picard.vcf.AccumulateVariantCallingMetrics
    • picard.sam.AddCommentsToBam
    • picard.sam.AddOrReplaceReadGroups
    • picard.util.BaitDesigner
    • picard.sam.BamIndexStats
    • picard.fastq.BamToBfq
    • picard.util.BedToIntervalList
    • picard.sam.BuildBamIndex
    • picard.sam.CalculateReadGroupChecksum
    • picard.fingerprint.CheckFingerprint
    • picard.illumina.CheckIlluminaDirectory
    • picard.sam.CheckTerminatorBlock
    • picard.sam.CleanSam
    • picard.fingerprint.ClusterCrosscheckMetrics
    • 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.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.analysis.CompareMetrics
    • picard.sam.CompareSAMs
    • picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
    • picard.sam.CreateSequenceDictionary
    • picard.fingerprint.CrosscheckFingerprints
      • picard.fingerprint.CrosscheckReadGroupFingerprints
    • picard.sam.DownsampleSam
    • picard.illumina.ExtractIlluminaBarcodes
    • 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.illumina.IlluminaBasecallsToFastq
    • picard.illumina.IlluminaBasecallsToSam
    • picard.util.IntervalListToBed
    • picard.util.IntervalListTools
    • picard.util.LiftOverIntervalList
    • picard.vcf.LiftoverVcf
    • picard.vcf.MakeSitesOnlyVcf
    • picard.illumina.MarkIlluminaAdapters
    • picard.sam.MergeBamAlignment
    • 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.util.ScatterIntervalsByNs
    • picard.sam.SetNmMdAndUqTags
      • picard.sam.SetNmAndUqTags
    • picard.analysis.SinglePassSamProgram
      • picard.analysis.CollectAlignmentSummaryMetrics
      • picard.analysis.CollectBaseDistributionByCycle
      • picard.analysis.CollectGcBiasMetrics
      • picard.analysis.CollectInsertSizeMetrics
      • picard.analysis.CollectQualityYieldMetrics
      • picard.analysis.CollectRnaSeqMetrics
      • picard.analysis.artifacts.CollectSequencingArtifactMetrics
      • picard.analysis.MeanQualityByCycle
      • picard.analysis.QualityScoreDistribution
    • picard.sam.SortSam
    • picard.vcf.SortVcf
    • picard.sam.SplitSamByLibrary
    • picard.vcf.SplitVcfs
    • picard.vcf.UpdateVcfSequenceDictionary
    • picard.sam.ValidateSamFile
    • picard.vcf.VcfFormatConverter
    • 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.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.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap (implements picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap)
  • org.broadinstitute.barclay.help.DocWorkUnitHandler
    • org.broadinstitute.barclay.help.DefaultDocWorkUnitHandler
      • picard.util.help.PicardHelpDocWorkUnitHandler
  • picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
  • picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader (implements java.util.Iterator<E>)
  • picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
  • picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor (implements java.lang.Runnable)
  • picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor.BarcodeMatch
  • picard.cmdline.programgroups.Fasta (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
  • picard.util.FileChannelJDKBugWorkAround
  • picard.illumina.parser.fakers.FileFaker
    • picard.illumina.parser.fakers.BarcodeFileFaker
    • picard.illumina.parser.fakers.BciFileFaker
    • picard.illumina.parser.fakers.BclFileFaker
    • 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.cmdline.programgroups.Fingerprinting (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
  • picard.fingerprint.FingerprintResults
  • picard.vcf.filter.FisherStrandFilter (implements picard.vcf.filter.VariantFilter)
  • picard.illumina.parser.FourChannelIntensityData
  • 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.util.GraphUtils
  • picard.util.GraphUtils.Graph<Node>
  • picard.fingerprint.HaplotypeBlock (implements java.lang.Comparable<T>)
  • picard.fingerprint.HaplotypeMap
  • picard.fingerprint.HaplotypeProbabilities
    • picard.fingerprint.HaplotypeProbabilitiesFromGenotype
    • picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
    • picard.fingerprint.HaplotypeProbabilitiesFromSequence
      • picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
    • picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
  • picard.util.help.HelpConstants
  • org.broadinstitute.barclay.help.HelpDoclet
    • picard.util.help.PicardHelpDoclet
  • picard.cmdline.programgroups.Illumina (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
  • picard.illumina.IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD>
  • picard.illumina.parser.IlluminaDataProviderFactory
  • picard.illumina.parser.IlluminaFileUtil
  • picard.fastq.IlluminaReadNameEncoder (implements picard.fastq.ReadNameEncoder)
  • picard.util.IlluminaUtil
  • 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.samtools.util.Locatable)
    • picard.annotation.Gene (implements java.lang.Iterable<T>)
  • picard.util.IntervalListScatterer
  • picard.cmdline.programgroups.Intervals (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
  • picard.util.Iterators
  • picard.illumina.LanePhasingMetricsCollector
  • picard.sam.markduplicates.util.LibraryIdGenerator
  • 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
  • htsjdk.samtools.metrics.MetricBase
    • picard.analysis.BaseDistributionByCycleMetrics
    • picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
    • picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
    • picard.analysis.CollectOxoGMetrics.CpcgMetrics
    • picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
    • picard.fingerprint.CrosscheckMetric
      • picard.fingerprint.ClusteredCrosscheckMetric
    • picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
    • picard.analysis.FingerprintingDetailMetrics
    • picard.analysis.FingerprintingSummaryMetrics
    • 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.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
        • picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
      • picard.analysis.CollectWgsMetrics.WgsMetrics
        • picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
        • picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
      • picard.sam.DuplicationMetrics
      • picard.analysis.artifacts.ErrorSummaryMetrics
      • picard.analysis.replicates.IndependentReplicateMetric
      • picard.vcf.MendelianViolations.MendelianViolationMetrics
    • picard.metrics.MultilevelMetrics
      • picard.analysis.AlignmentSummaryMetrics
      • picard.analysis.GcBiasDetailMetrics
      • picard.analysis.GcBiasSummaryMetrics
      • picard.analysis.directed.HsMetrics
      • picard.analysis.InsertSizeMetrics
      • picard.analysis.RnaSeqMetrics
      • picard.analysis.RrbsCpgDetailMetrics
      • picard.analysis.RrbsSummaryMetrics
      • picard.analysis.directed.TargetedPcrMetrics
    • picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
    • picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
    • picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
    • picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
    • picard.sam.markduplicates.UmiMetrics
  • picard.cmdline.programgroups.Metrics (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
  • 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.illumina.NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD>
  • picard.cmdline.programgroups.None (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
  • picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
  • picard.illumina.parser.OutputMapping
  • 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.PerTilePerCycleFileUtil
  • picard.pedigree.PedFile.PedTrio
  • picard.illumina.parser.PerTileParser<ILLUMINA_DATA>
    • picard.illumina.parser.PosParser
  • 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.cmdline.PicardCommandLine
  • picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator<T> (implements htsjdk.samtools.util.CloseableIterator<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.illumina.parser.ReadData
  • 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
    • picard.sam.markduplicates.util.OpticalDuplicateFinder
  • picard.illumina.parser.ReadStructure
  • picard.illumina.parser.ReadStructure.Substructure (implements java.lang.Iterable<T>)
  • picard.annotation.RefFlatReader
  • picard.util.ReflectionUtil
  • picard.sam.ReorderSam.ReorderSamReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
  • picard.sam.util.RepresentativeReadIndexer
  • picard.sam.markduplicates.util.RepresentativeReadIndexerCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
  • 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.cmdline.programgroups.SamOrBam (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
  • picard.metrics.SAMRecordAndReference
  • htsjdk.samtools.util.SamRecordWithOrdinal
    • picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
  • picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
  • picard.analysis.artifacts.SequencingArtifactMetrics
  • picard.fingerprint.Snp (implements java.lang.Comparable<T>)
  • picard.cmdline.StandardOptionDefinitions
  • picard.util.TabbedTextFileWithHeaderParser (implements 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
  • 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.vcf.processor.VariantIteratorProducer
  • picard.vcf.processor.VariantProcessor<RESULT,ACCUMULATOR>
  • picard.vcf.processor.VariantProcessor.Builder<A,R>
  • picard.vcf.processor.VcfFileSegment
  • picard.vcf.processor.VcfFileSegmentGenerator
  • picard.cmdline.programgroups.VcfOrBcf (implements org.broadinstitute.barclay.argparser.CommandLineProgramGroup)
  • picard.vcf.VcfUtils
  • picard.analysis.WgsMetricsProcessorImpl<T> (implements picard.analysis.WgsMetricsProcessor)

Interface Hierarchy

• picard.util.AdapterPair
• picard.util.AtomicIterator<T>
• picard.analysis.CollectMultipleMetrics.ProgramInterface
• picard.cmdline.CommandLineProgramGroup
• picard.vcf.filter.GenotypeFilter
• picard.cmdline.argumentcollections.IntervalArgumentCollection
• picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>
• picard.sam.util.PhysicalLocation
• picard.sam.PrimaryAlignmentSelectionStrategy
• picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
• picard.fastq.ReadNameEncoder
• picard.cmdline.argumentcollections.ReferenceArgumentCollection
• 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.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
    • picard.analysis.CollectMultipleMetrics.Program (implements picard.analysis.CollectMultipleMetrics.ProgramInterface)
    • picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
    • picard.fingerprint.CrosscheckMetric.DataType
    • picard.fingerprint.CrosscheckMetric.FingerprintResult
    • picard.fingerprint.DiploidGenotype
    • picard.fingerprint.DiploidHaplotype
    • picard.sam.FilterSamReads.Filter
    • 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.illumina.parser.IlluminaMetricsCode
    • picard.util.IlluminaUtil.IlluminaAdapterPair (implements picard.util.AdapterPair)
    • picard.illumina.parser.IntensityChannel
    • picard.util.IntervalListScatterer.Mode
    • 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.illumina.parser.ReadType
    • picard.annotation.RefFlatReader.RefFlatColumns
    • picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
    • picard.sam.RevertSam.FileType
    • picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
    • picard.pedigree.Sex
    • picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
    • picard.illumina.parser.TileTemplateRead
    • picard.sam.ValidateSamFile.Mode
    • picard.util.VariantType
    • picard.sam.ViewSam.AlignmentStatus
    • picard.sam.ViewSam.PfStatus