# Hierarchy For Package picard.sam

Package Hierarchies:

- All Packages

## Class Hierarchy

- java.lang.Object
  - picard.sam.AbstractAlignmentMerger
    - picard.sam.SamAlignmentMerger
  - picard.sam.BestEndMapqPrimaryAlignmentStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
  - picard.sam.BestMapqPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
  - picard.cmdline.CommandLineProgram
    - picard.sam.AddCommentsToBam
    - picard.sam.AddOrReplaceReadGroups
    - picard.sam.BamIndexStats
    - picard.sam.BuildBamIndex
    - picard.sam.CalculateReadGroupChecksum
    - picard.sam.CheckTerminatorBlock
    - picard.sam.CleanSam
    - picard.sam.CompareSAMs
    - picard.sam.CreateSequenceDictionary
    - picard.sam.DownsampleSam
    - picard.sam.FastqToSam
    - picard.sam.FilterSamReads
    - picard.sam.FixMateInformation
    - picard.sam.GatherBamFiles
    - picard.sam.MergeBamAlignment
    - picard.sam.MergeSamFiles
    - picard.sam.PositionBasedDownsampleSam
    - picard.sam.ReorderSam
    - picard.sam.ReplaceSamHeader
    - picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
    - picard.sam.RevertSam
    - picard.sam.SamFormatConverter
    - picard.sam.SamToFastq
    - picard.sam.SetNmMdAndUqTags
      - picard.sam.SetNmAndUqTags
    - picard.sam.SortSam
    - picard.sam.SplitSamByLibrary
    - picard.sam.ValidateSamFile
    - picard.sam.ViewSam
  - picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
  - htsjdk.samtools.metrics.MetricBase
    - picard.analysis.MergeableMetricBase
      - picard.sam.DuplicationMetrics
  - picard.sam.MostDistantPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)

## Interface Hierarchy

- picard.sam.PrimaryAlignmentSelectionStrategy

## Enum Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    - picard.sam.FilterSamReads.Filter
    - picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
    - picard.sam.RevertSam.FileType
    - picard.sam.ValidateSamFile.Mode
    - picard.sam.ViewSam.AlignmentStatus
    - picard.sam.ViewSam.PfStatus