picard.sam.markduplicates.util

Class ReadEndsForMarkDuplicates

java.lang.Object

picard.sam.util.PhysicalLocationInt

picard.sam.util.PhysicalLocationShort

picard.sam.markduplicates.util.ReadEnds

picard.sam.markduplicates.util.ReadEndsForMarkDuplicates

All Implemented Interfaces:

java.lang.Cloneable, PhysicalLocation

Direct Known Subclasses:

ReadEndsForMarkDuplicatesWithBarcodes

public class ReadEndsForMarkDuplicates
extends ReadEnds
implements java.lang.Cloneable

Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar

Author:

Nils Homer

Field Summary

Fields

Modifier and Type	Field and Description
long	read1IndexInFile
long	read2IndexInFile
short	score
protected static int	SIZE_OF

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
ReadEndsForMarkDuplicates()
ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates read)

Method Summary

Modifier and Type	Method and Description
ReadEndsForMarkDuplicates	clone()
static int	getSizeOf()

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

getLibraryId, getOrientationByte, getReadGroup, isPaired, 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

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

Methods inherited from interface picard.sam.util.PhysicalLocation

hasLocation

Field Detail

SIZE_OF

protected static final int SIZE_OF

See Also:

Constant Field Values

score

public short score

read1IndexInFile

public long read1IndexInFile

read2IndexInFile

public long read2IndexInFile

Constructor Detail

ReadEndsForMarkDuplicates

public ReadEndsForMarkDuplicates()

ReadEndsForMarkDuplicates

public ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates read)

Method Detail

getSizeOf

public static int getSizeOf()

clone

public ReadEndsForMarkDuplicates clone()

Overrides:

clone in class java.lang.Object