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.