picard.sam.markduplicates.util

Class ReadEndsForMarkDuplicatesWithBarcodes

java.lang.Object

picard.sam.util.PhysicalLocationInt

picard.sam.util.PhysicalLocationShort

picard.sam.markduplicates.util.ReadEnds

picard.sam.markduplicates.util.ReadEndsForMarkDuplicates

picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes

All Implemented Interfaces:

java.lang.Cloneable, PhysicalLocation

public class ReadEndsForMarkDuplicatesWithBarcodes
extends ReadEndsForMarkDuplicates

Field Summary

Fields

Modifier and Type	Field and Description
int	barcode
int	readOneBarcode
int	readTwoBarcode

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

read1IndexInFile, read2IndexInFile, score, 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
ReadEndsForMarkDuplicatesWithBarcodes()
ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates read)
ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes read)

Method Summary

Modifier and Type	Method and Description
ReadEndsForMarkDuplicatesWithBarcodes	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

barcode

public int barcode

readOneBarcode

public int readOneBarcode

readTwoBarcode

public int readTwoBarcode

Constructor Detail

ReadEndsForMarkDuplicatesWithBarcodes

public ReadEndsForMarkDuplicatesWithBarcodes()

ReadEndsForMarkDuplicatesWithBarcodes

public ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates read)

ReadEndsForMarkDuplicatesWithBarcodes

public ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes read)

Method Detail

clone

public ReadEndsForMarkDuplicatesWithBarcodes clone()

Overrides:

clone in class ReadEndsForMarkDuplicates

getSizeOf

public static int getSizeOf()