# Package picard.sam.markduplicates.util

- Interface Summary
  Interface | Description
  --- | ---
  ReadEndsForMarkDuplicatesMap | Interface for storing and retrieving ReadEnds objects.

- Class Summary
  Class | Description
  --- | ---
  AbstractMarkDuplicatesCommandLineProgram | Abstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM files.
  AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator | Little class used to package up a header and an iterable/iterator.
  AbstractOpticalDuplicateFinderCommandLineProgram | Abstract class that holds parameters and methods common to classes that optical duplicate detection.
  DiskBasedReadEndsForMarkDuplicatesMap | Disk-based implementation of ReadEndsForMarkDuplicatesMap.
  LibraryIdGenerator | A class to generate library Ids and keep duplication metrics by library IDs.
  MarkQueue | This is the mark queue.
  OpticalDuplicateFinder | Contains methods for finding optical/co-localized/sequencing duplicates.
  PhysicalLocationForMateCigar | Stores the minimal information needed for optical duplicate detection.
  PhysicalLocationForMateCigarSet | This stores records that are comparable for detecting optical duplicates.
  ReadEnds | Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
  ReadEndsForMarkDuplicates | Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
  ReadEndsForMarkDuplicatesCodec | Codec for ReadEnds that just outputs the primitive fields and reads them back.
  ReadEndsForMarkDuplicatesWithBarcodes |
  ReadEndsForMarkDuplicatesWithBarcodesCodec | Created by nhomer on 9/13/15.
  ReadEndsForMateCigar | A class to store individual records for MarkDuplicatesWithMateCigar.
  SamRecordWithOrdinalAndSetDuplicateReadFlag | This class sets the duplicate read flag as the result state when examining sets of records.