# Package picard.sam.markduplicates

- Class Summary
  Class | Description
  --- | ---
  CheckDuplicateMarking |
  CollectDuplicateMetrics | Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.
  EstimateLibraryComplexity | Attempts to estimate library complexity from sequence alone.
  MarkDuplicates | A better duplication marking algorithm that handles all cases including clipped and gapped alignments.
  MarkDuplicatesWithMateCigar | An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.
  MarkDuplicatesWithMateCigarIterator | This will iterate through a coordinate sorted SAM file (iterator) and either mark or remove duplicates as appropriate.
  SimpleMarkDuplicatesWithMateCigar | This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.
  UmiAwareMarkDuplicatesWithMateCigar | This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
  UmiGraph | UmiGraph is used to identify UMIs that come from the same original source molecule.
  UmiMetrics | Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.

- Enum Summary
  Enum | Description
  --- | ---
  CheckDuplicateMarking.Mode |
  MarkDuplicates.DuplicateTaggingPolicy | Enum used to control how duplicates are flagged in the DT optional tag on each read.
  MarkDuplicates.DuplicateType | Enum for the possible values that a duplicate read can be tagged with in the DT attribute.