ReadEndsForMarkDuplicatesWithBarcodes (picard 3.5.0 API)

java.lang.Object

picard.sam.util.PhysicalLocationInt

picard.sam.markduplicates.util.ReadEnds

picard.sam.markduplicates.util.ReadEndsForMarkDuplicates

picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes

All Implemented Interfaces:: Serializable, Cloneable, PhysicalLocation

public class ReadEndsForMarkDuplicatesWithBarcodes extends ReadEndsForMarkDuplicates

See Also:

Field Summary

Fields

Modifier and Type

Field

Description

int

barcode

int

readOneBarcode

int

readTwoBarcode

Fields inherited from class ReadEndsForMarkDuplicates
duplicateSetSize, read1IndexInFile, read2IndexInFile, score, SIZE_OF

Fields inherited from class ReadEnds
F, FF, FR, isOpticalDuplicate, libraryId, orientation, orientationForOpticalDuplicates, R, read1Coordinate, read1ReferenceIndex, read2Coordinate, read2ReferenceIndex, readGroup, RF, RR

Fields inherited from class PhysicalLocationInt
tile, x, y

Fields inherited from interface PhysicalLocation
NO_VALUE
Constructor Summary

Constructors

Constructor

Description

ReadEndsForMarkDuplicatesWithBarcodes()

ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates read)

ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes read)
Method Summary

Modifier and Type

Method

Description

ReadEndsForMarkDuplicatesWithBarcodes

clone()

static int

getSizeOf()

Methods inherited from class ReadEndsForMarkDuplicates
isSingleEndReadKnownFragment, toString

Methods inherited from class ReadEnds
getLibraryId, getOrientationByte, getReadGroup, isPaired, setLibraryId, setReadGroup

Methods inherited from class PhysicalLocationInt
getTile, getX, getY, setTile, setX, setY

Methods inherited from class Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface PhysicalLocation
hasLocation

Field Details
- barcode
  
  public int barcode
- readOneBarcode
  
  public int readOneBarcode
- readTwoBarcode
  
  public int readTwoBarcode
Constructor Details
- ReadEndsForMarkDuplicatesWithBarcodes
  
  public ReadEndsForMarkDuplicatesWithBarcodes()
- ReadEndsForMarkDuplicatesWithBarcodes
  
  public ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates read)
- ReadEndsForMarkDuplicatesWithBarcodes
  
  public ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes read)
Method Details
- clone
  
  public ReadEndsForMarkDuplicatesWithBarcodes clone()
  
  Overrides:
  
  clone in class ReadEndsForMarkDuplicates
- getSizeOf
  
  public static int getSizeOf()