# Hierarchy For Package picard.analysis

Package Hierarchies:

- All Packages

## Class Hierarchy

- java.lang.Object
  - picard.analysis.AdapterUtility
  - picard.analysis.ChimeraUtil
  - picard.analysis.CollectWgsMetrics.WgsMetricsCollector
    - picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
  - picard.cmdline.CommandLineProgram
    - picard.analysis.CollectJumpingLibraryMetrics
    - picard.analysis.CollectMultipleMetrics
    - picard.analysis.CollectOxoGMetrics
    - picard.analysis.CollectRrbsMetrics
    - picard.analysis.CollectWgsMetrics
      - picard.analysis.CollectRawWgsMetrics
      - picard.analysis.CollectWgsMetricsFromSampledSites
      - picard.analysis.CollectWgsMetricsWithNonZeroCoverage
    - picard.analysis.CollectWgsMetricsFromQuerySorted
    - picard.analysis.CompareMetrics
    - picard.analysis.SinglePassSamProgram
      - picard.analysis.CollectAlignmentSummaryMetrics
      - picard.analysis.CollectBaseDistributionByCycle
      - picard.analysis.CollectGcBiasMetrics
      - picard.analysis.CollectInsertSizeMetrics
      - picard.analysis.CollectQualityYieldMetrics
      - picard.analysis.CollectRnaSeqMetrics
      - picard.analysis.MeanQualityByCycle
      - picard.analysis.QualityScoreDistribution
  - 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.CollectQualityYieldMetrics.QualityYieldMetrics
    - picard.analysis.FingerprintingDetailMetrics
    - picard.analysis.FingerprintingSummaryMetrics
    - picard.analysis.JumpingLibraryMetrics
    - picard.analysis.MergeableMetricBase
      - picard.analysis.CollectWgsMetrics.WgsMetrics
        - picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
        - picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
        - picard.analysis.CollectWgsMetricsFromSampledSites.SampledWgsMetrics
        - 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.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

## Interface Hierarchy

- picard.analysis.CollectMultipleMetrics.ProgramInterface

## 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.analysis.AlignmentSummaryMetrics.Category
    - picard.analysis.CollectMultipleMetrics.Program (implements picard.analysis.CollectMultipleMetrics.ProgramInterface)
    - picard.analysis.CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY
    - picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
    - picard.analysis.MetricAccumulationLevel