# Hierarchy For Package picard.sam.markduplicates

Package Hierarchies:

- All Packages

## Class Hierarchy

- java.lang.Object
  - 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.sam.markduplicates.CheckDuplicateMarking
    - picard.analysis.SinglePassSamProgram
      - picard.sam.markduplicates.CollectDuplicateMetrics
  - picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
  - picard.sam.markduplicates.MarkDuplicatesForFlowHelper (implements picard.sam.markduplicates.MarkDuplicatesHelper)
  - picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator (implements htsjdk.samtools.SAMRecordIterator)
  - htsjdk.samtools.metrics.MetricBase
    - picard.sam.markduplicates.UmiMetrics
  - picard.sam.markduplicates.UmiGraph

## Interface Hierarchy

- picard.sam.markduplicates.MarkDuplicatesHelper

## Enum Class Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    - picard.sam.markduplicates.CheckDuplicateMarking.Mode (implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum)
    - picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
    - picard.sam.markduplicates.MarkDuplicates.DuplicateType
    - picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection.FLOW_DUPLICATE_SELECTION_STRATEGY