picard.sam.markduplicates.util

Class MarkQueue

java.lang.Object

picard.sam.markduplicates.util.MarkQueue

public class MarkQueue
extends java.lang.Object

This is the mark queue.

This stores a current nonDuplicateReadEndsSet of read ends that need to be duplicate marked. It only stores internally the "best" read end for a given possible duplicate location, preferring to perform duplicate marking as read ends come in, rather than wait for all "comparable" read ends to arrive. This reduces the memory footprint of this data structure.

Constructor Summary

Constructors

Constructor and Description
MarkQueue(htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy)

Method Summary

Modifier and Type	Method and Description
void	add(ReadEndsForMateCigar other, htsjdk.samtools.util.SamRecordTrackingBuffer outputBuffer, DuplicationMetrics metrics) Add a record to the mark queue.
java.util.Set<ReadEnds>	getLocations(ReadEndsForMateCigar current) Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
int	getNumDuplicates() Returns the number of duplicates detected
int	getToMarkQueueMinimumDistance() Returns the minimum genomic distance such that we can be assured that all duplicates have been considered.
boolean	isEmpty()
ReadEndsForMateCigar	peek() Returns the first element in this queue
ReadEndsForMateCigar	poll(htsjdk.samtools.util.SamRecordTrackingBuffer outputBuffer, htsjdk.samtools.SAMFileHeader header, OpticalDuplicateFinder opticalDuplicateFinder, LibraryIdGenerator libraryIdGenerator) The poll method will return the read end that is *not* the duplicate of all comparable read ends that have been seen.
void	setToMarkQueueMinimumDistance(int toMarkQueueMinimumDistance) Sets the minimum genomic distance such that we can be assured that all duplicates have been considered.
boolean	shouldBeInLocations(ReadEndsForMateCigar current) Returns true if we should track this for optical duplicate detection, false otherwise
int	size() The number of records currently in this queue.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MarkQueue

public MarkQueue(htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy)

Method Detail

getNumDuplicates

public int getNumDuplicates()

Returns the number of duplicates detected

size

public int size()

The number of records currently in this queue. *

isEmpty

public boolean isEmpty()

setToMarkQueueMinimumDistance

public void setToMarkQueueMinimumDistance(int toMarkQueueMinimumDistance)

Sets the minimum genomic distance such that we can be assured that all duplicates have been considered.

getToMarkQueueMinimumDistance

public int getToMarkQueueMinimumDistance()

Returns the minimum genomic distance such that we can be assured that all duplicates have been considered.

shouldBeInLocations

public boolean shouldBeInLocations(ReadEndsForMateCigar current)

Returns true if we should track this for optical duplicate detection, false otherwise

getLocations

public java.util.Set<ReadEnds> getLocations(ReadEndsForMateCigar current)

Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.

peek

public ReadEndsForMateCigar peek()

Returns the first element in this queue

poll

public ReadEndsForMateCigar poll(htsjdk.samtools.util.SamRecordTrackingBuffer outputBuffer,
                                 htsjdk.samtools.SAMFileHeader header,
                                 OpticalDuplicateFinder opticalDuplicateFinder,
                                 LibraryIdGenerator libraryIdGenerator)

The poll method will return the read end that is *not* the duplicate of all comparable read ends that have been seen. All comparable read ends and the returned read end will have their seen duplicate flag nonDuplicateReadEndsSet. We use the minimum genomic distance to determine when all the comparable reads have been examined.

add

public void add(ReadEndsForMateCigar other,
                htsjdk.samtools.util.SamRecordTrackingBuffer outputBuffer,
                DuplicationMetrics metrics)

Add a record to the mark queue.