Package picard.sam.markduplicates.util
package picard.sam.markduplicates.util
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ClassDescriptionAbstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM/CRAM files.Little class used to package up a header and an iterable/iterator.Abstract class that holds parameters and methods common to classes that optical duplicate detection.Disk-based implementation of ReadEndsForMarkDuplicatesMap.A class to generate library Ids and keep duplication metrics by library IDs.This is the mark queue.Map from String to ReadEnds object.Contains methods for finding optical/co-localized/sequencing duplicates.Stores the minimal information needed for optical duplicate detection.This stores records that are comparable for detecting optical duplicates.Little struct-like class to hold read pair (and fragment) end data for duplicate marking.Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigarCodec for ReadEnds that just outputs the primitive fields and reads them back.Interface for storing and retrieving ReadEnds objects.Created by nhomer on 9/13/15.A class to store individual records for MarkDuplicatesWithMateCigar.Codec for read names and integers that outputs the primitive fields and reads them back.This class sets the duplicate read flag as the result state when examining sets of records.