htsjdk.samtools

Class DuplicateSet

java.lang.Object

htsjdk.samtools.DuplicateSet

public class DuplicateSet
extends java.lang.Object

Stores a set of records that are duplicates of each other. The first records in the list of records is considered the representative of the duplicate, and typically does not have it's duplicate flag set. The records' duplicate flag will be set appropriately as records are added. This behavior can be turned off. At this time, this set does not track optical duplicates.

Constructor Summary

Constructors

Constructor and Description
DuplicateSet() Sets the duplicate flag by default
DuplicateSet(boolean setDuplicateFlag)
DuplicateSet(boolean setDuplicateFlag, SAMRecordDuplicateComparator comparator)
DuplicateSet(SAMRecordDuplicateComparator comparator)

Method Summary

Modifier and Type	Method and Description
int	add(SAMRecord record) Adds a record to the set and returns zero if either the set is empty, or it is a duplicate of the records already in the set.
java.util.List<SAMRecord>	getRecords() Gets the list of records from this set.
java.util.List<SAMRecord>	getRecords(boolean sort) Gets the list of records from this set.
SAMRecord	getRepresentative() Gets the representative record according to the duplicate comparator.
boolean	isEmpty()
int	numDuplicates() Returns the number of duplicates in this set, including the representative record.
void	setDuplicateFlag(boolean setDuplicateFlag) Controls if we should update the duplicate flag of the records in this set.
int	size() Returns the number of records in this set.

Methods inherited from class java.lang.Object

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

Constructor Detail

DuplicateSet

public DuplicateSet()

Sets the duplicate flag by default

DuplicateSet

public DuplicateSet(boolean setDuplicateFlag)

DuplicateSet

public DuplicateSet(SAMRecordDuplicateComparator comparator)

DuplicateSet

public DuplicateSet(boolean setDuplicateFlag,
                    SAMRecordDuplicateComparator comparator)

Method Detail

add

public int add(SAMRecord record)

Adds a record to the set and returns zero if either the set is empty, or it is a duplicate of the records already in the set. Otherwise, it does not add the record and returns non-zero.

Parameters:

record - the record to add.

Returns:

zero if the record belongs in this set, -1 in a previous set, or 1 in a subsequent set, according to the comparison order

getRecords

public java.util.List<SAMRecord> getRecords(boolean sort)

Gets the list of records from this set. Setting sort to false likely will not yield records in duplicate order within the set.

Parameters:

sort - true if we want the records in the duplicate set sorted by duplicate order, false if we do not care about the order.

getRecords

public java.util.List<SAMRecord> getRecords()

Gets the list of records from this set.

getRepresentative

public SAMRecord getRepresentative()

Gets the representative record according to the duplicate comparator.

size

public int size()

Returns the number of records in this set.

numDuplicates

public int numDuplicates()

Returns the number of duplicates in this set, including the representative record. Does not include records that are unmapped, secondary, or supplementary.

isEmpty

public boolean isEmpty()

setDuplicateFlag

public void setDuplicateFlag(boolean setDuplicateFlag)

Controls if we should update the duplicate flag of the records in this set.