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 picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
duplicateSetSize, 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

Description

ReadEndsForMarkDuplicatesWithBarcodes()

ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates read)

ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes read)
Method Summary

Modifier and Type

Method

Description

ReadEndsForMarkDuplicatesWithBarcodes

clone()

static int

getSizeOf()

Methods inherited from class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
isSingleEndReadKnownFragment, toString

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, wait, wait, wait

Methods inherited from interface picard.sam.util.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()

Class ReadEndsForMarkDuplicatesWithBarcodes

Field Summary

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

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

Fields inherited from class picard.sam.util.PhysicalLocationInt

Fields inherited from interface picard.sam.util.PhysicalLocation

Constructor Summary

Method Summary

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

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

Methods inherited from class picard.sam.util.PhysicalLocationShort

Methods inherited from class picard.sam.util.PhysicalLocationInt

Methods inherited from class java.lang.Object

Methods inherited from interface picard.sam.util.PhysicalLocation

Field Details

barcode

readOneBarcode

readTwoBarcode

Constructor Details

ReadEndsForMarkDuplicatesWithBarcodes

ReadEndsForMarkDuplicatesWithBarcodes

ReadEndsForMarkDuplicatesWithBarcodes

Method Details

clone

getSizeOf