picard.sam.markduplicates.util

Class PhysicalLocationForMateCigar

java.lang.Object

picard.sam.util.PhysicalLocationInt

picard.sam.util.PhysicalLocationShort

picard.sam.markduplicates.util.PhysicalLocationForMateCigar

All Implemented Interfaces:

PhysicalLocation

public class PhysicalLocationForMateCigar
extends PhysicalLocationShort

Stores the minimal information needed for optical duplicate detection.

Field Summary

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
PhysicalLocationForMateCigar(PhysicalLocation rec)

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object other)
short	getLibraryId()
short	getReadGroup()
int	hashCode()
void	setLibraryId(short libraryId)
void	setReadGroup(short rg)

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

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

Methods inherited from interface picard.sam.util.PhysicalLocation

hasLocation

Constructor Detail

PhysicalLocationForMateCigar

public PhysicalLocationForMateCigar(PhysicalLocation rec)

Method Detail

getReadGroup

public short getReadGroup()

Specified by:

getReadGroup in interface PhysicalLocation

Overrides:

getReadGroup in class PhysicalLocationInt

setReadGroup

public void setReadGroup(short rg)

Specified by:

setReadGroup in interface PhysicalLocation

Overrides:

setReadGroup in class PhysicalLocationInt

getLibraryId

public short getLibraryId()

Specified by:

getLibraryId in interface PhysicalLocation

Overrides:

getLibraryId in class PhysicalLocationInt

setLibraryId

public void setLibraryId(short libraryId)

Specified by:

setLibraryId in interface PhysicalLocation

Overrides:

setLibraryId in class PhysicalLocationInt

equals

public boolean equals(java.lang.Object other)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object