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.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)
  • picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
  • htsjdk.samtools.metrics.MetricBase
    • picard.analysis.MergeableMetricBase
      • picard.sam.DuplicationMetrics
  • picard.sam.MostDistantPrimaryAlignmentSelectionStrategy (implements picard.sam.PrimaryAlignmentSelectionStrategy)
  • picard.sam.ReorderSam.ReorderSamReferenceArgumentCollection (implements picard.cmdline.argumentcollections.ReferenceArgumentCollection)

Interface Hierarchy

• picard.sam.PrimaryAlignmentSelectionStrategy

Enum Hierarchy

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