# Hierarchy For Package picard.analysis

Package Hierarchies:

- All Packages

## Class Hierarchy

- java.lang.Object
  - picard.analysis.AbstractWgsMetricsCollector<T>
    - picard.analysis.CollectWgsMetrics.WgsMetricsCollector
      - picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
    - picard.analysis.FastWgsMetricsCollector
  - 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.analysis.ChimeraUtil
  - picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
  - 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.CommandLineProgram
    - picard.analysis.CollectJumpingLibraryMetrics
    - picard.analysis.CollectMultipleMetrics
    - picard.analysis.CollectOxoGMetrics
    - picard.analysis.CollectRrbsMetrics
    - picard.analysis.CollectWgsMetrics
      - picard.analysis.CollectRawWgsMetrics
      - picard.analysis.CollectWgsMetricsWithNonZeroCoverage
    - picard.analysis.CompareMetrics
    - picard.analysis.SinglePassSamProgram
      - picard.analysis.CollectAlignmentSummaryMetrics
      - picard.analysis.CollectBaseDistributionByCycle
      - picard.analysis.CollectGcBiasMetrics
      - picard.analysis.CollectInsertSizeMetrics
      - picard.analysis.CollectQualityYieldMetrics
      - picard.analysis.CollectQualityYieldMetricsFlow
      - picard.analysis.CollectQualityYieldMetricsSNVQ
      - picard.analysis.CollectRnaSeqMetrics
      - picard.analysis.MeanQualityByCycle
      - picard.analysis.QualityScoreDistribution
  - picard.analysis.CounterManager
  - picard.analysis.CounterManager.Counter
  - picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector (implements picard.metrics.PerUnitMetricCollector<BEAN,HKEY,ARGTYPE>)
  - picard.analysis.GcBiasUtils
  - htsjdk.samtools.metrics.MetricBase
    - picard.analysis.BaseDistributionByCycleMetrics
    - picard.analysis.CollectOxoGMetrics.CpcgMetrics
    - picard.analysis.CompareMetrics.MetricComparisonDifferences
    - picard.analysis.FingerprintingDetailMetrics
    - picard.analysis.FingerprintingSummaryMetrics
    - picard.analysis.JumpingLibraryMetrics
    - picard.analysis.MergeableMetricBase
      - picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
      - picard.analysis.CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow
      - picard.analysis.CollectQualityYieldMetricsSNVQ.QualityYieldMetrics
      - 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.RnaSeqMetrics
      - picard.analysis.RrbsCpgDetailMetrics
      - picard.analysis.RrbsSummaryMetrics
    - picard.analysis.TheoreticalSensitivityMetrics
  - picard.metrics.MultiLevelCollector<METRIC_TYPE,Histogram_KEY,ARGTYPE>
    - picard.analysis.GcBiasMetricsCollector
    - picard.metrics.SAMRecordAndReferenceMultiLevelCollector<BEAN,HKEY>
      - picard.analysis.AlignmentSummaryMetricsCollector
      - picard.analysis.RrbsMetricsCollector
  - picard.analysis.TheoreticalSensitivity
  - picard.analysis.TheoreticalSensitivity.RouletteWheel
  - picard.analysis.WgsMetricsProcessorImpl<T> (implements picard.analysis.WgsMetricsProcessor)

## Interface Hierarchy

- picard.analysis.CollectMultipleMetrics.ProgramInterface
- 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.analysis.AlignmentSummaryMetrics.Category
    - picard.analysis.CollectMultipleMetrics.Program (implements picard.analysis.CollectMultipleMetrics.ProgramInterface, org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
    - picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
    - picard.analysis.MetricAccumulationLevel