picard.sam.markduplicates.util

Class ReadEndsForMarkDuplicates

java.lang.Object

picard.sam.markduplicates.util.ReadEnds

picard.sam.markduplicates.util.ReadEndsForMarkDuplicates

All Implemented Interfaces:

OpticalDuplicateFinder.PhysicalLocation

public class ReadEndsForMarkDuplicates
extends ReadEnds

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

Field Summary

Fields

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

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

F, FF, FR, libraryId, orientation, orientationForOpticalDuplicates, R, read1Coordinate, read1ReferenceIndex, read2Coordinate, read2ReferenceIndex, readGroup, RF, RR, tile, x, y

Constructor Summary

Constructors

Constructor and Description
ReadEndsForMarkDuplicates()

Method Summary

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

getLibraryId, getOrientationByte, getReadGroup, getTile, getX, getY, isPaired, setLibraryId, setReadGroup, setTile, setX, setY

Methods inherited from class java.lang.Object

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

Field Detail

SIZE_OF

public 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()