picard.sam.markduplicates.util

Class ReadEndsForMateCigar

java.lang.Object

picard.sam.util.PhysicalLocationInt

picard.sam.util.PhysicalLocationShort

picard.sam.markduplicates.util.ReadEnds

picard.sam.markduplicates.util.ReadEndsForMateCigar

All Implemented Interfaces:

PhysicalLocation

public class ReadEndsForMateCigar
extends ReadEnds

A class to store individual records for MarkDuplicatesWithMateCigar. This aids in comparing records to determine which need to be compared when we mark duplicates. We also store the original SAMRecord and its ordinal in the input file (in SamRecordWithOrdinal) to access optional tags (mate cigar) and other information.

Field Summary

Fields

Modifier and Type	Field and Description
htsjdk.samtools.util.SamRecordWithOrdinal	samRecordWithOrdinal

Fields inherited from class picard.sam.markduplicates.util.ReadEnds

F, FF, FR, isOpticalDuplicate, libraryId, orientation, orientationForOpticalDuplicates, R, read1Coordinate, read1ReferenceIndex, read2Coordinate, read2ReferenceIndex, readGroup, RF, RR

Fields inherited from class picard.sam.util.PhysicalLocationInt

tile, x, y

Fields inherited from interface picard.sam.util.PhysicalLocation

NO_VALUE

Constructor Summary

Constructors

Constructor and Description
ReadEndsForMateCigar(ReadEndsForMateCigar other, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal) Creates a shallow copy from the "other"
ReadEndsForMateCigar(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal, OpticalDuplicateFinder opticalDuplicateFinder, short libraryId) Builds a read ends object that represents a single read.

Method Summary

Modifier and Type	Method and Description
PhysicalLocationForMateCigarSet	getLocationSet()
java.util.Set<ReadEnds>	getReadEndSetForOpticalDuplicates() Gets the read ends for optical duplicate tracking
htsjdk.samtools.SAMRecord	getRecord()
java.lang.String	getRecordReadName()
htsjdk.samtools.util.SamRecordWithOrdinal	getSamRecordIndex() A number of convenience functions
boolean	isPaired()
PhysicalLocationForMateCigarSet	removeLocationSet()
void	setLocationSet(PhysicalLocationForMateCigarSet locationSet)

Methods inherited from class picard.sam.markduplicates.util.ReadEnds

getLibraryId, getOrientationByte, getReadGroup, setLibraryId, setReadGroup

Methods inherited from class picard.sam.util.PhysicalLocationShort

setX, setY

Methods inherited from class picard.sam.util.PhysicalLocationInt

getTile, getX, getY, setTile

Methods inherited from class java.lang.Object

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

Methods inherited from interface picard.sam.util.PhysicalLocation

hasLocation

Field Detail

samRecordWithOrdinal

public htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal

Constructor Detail

ReadEndsForMateCigar

public ReadEndsForMateCigar(htsjdk.samtools.SAMFileHeader header,
                            htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal,
                            OpticalDuplicateFinder opticalDuplicateFinder,
                            short libraryId)

Builds a read ends object that represents a single read.

ReadEndsForMateCigar

public ReadEndsForMateCigar(ReadEndsForMateCigar other,
                            htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal)

Creates a shallow copy from the "other"

Method Detail

getSamRecordIndex

public htsjdk.samtools.util.SamRecordWithOrdinal getSamRecordIndex()

A number of convenience functions

getRecord

public htsjdk.samtools.SAMRecord getRecord()

getRecordReadName

public java.lang.String getRecordReadName()

isPaired

public boolean isPaired()

Overrides:

isPaired in class ReadEnds

getReadEndSetForOpticalDuplicates

public java.util.Set<ReadEnds> getReadEndSetForOpticalDuplicates()

Gets the read ends for optical duplicate tracking

getLocationSet

public PhysicalLocationForMateCigarSet getLocationSet()

removeLocationSet

public PhysicalLocationForMateCigarSet removeLocationSet()

setLocationSet

public void setLocationSet(PhysicalLocationForMateCigarSet locationSet)