picard.sam.markduplicates.util

Class PhysicalLocationForMateCigar

java.lang.Object

picard.sam.markduplicates.util.PhysicalLocationForMateCigar

All Implemented Interfaces:

OpticalDuplicateFinder.PhysicalLocation

public class PhysicalLocationForMateCigar
extends java.lang.Object
implements OpticalDuplicateFinder.PhysicalLocation

Stores the minimal information needed for optical duplicate detection.

Constructor Summary

Constructors

Constructor and Description
PhysicalLocationForMateCigar(OpticalDuplicateFinder.PhysicalLocation rec)

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object other)
short	getLibraryId()
short	getReadGroup()
short	getTile()
short	getX()
short	getY()
int	hashCode()
void	setLibraryId(short libraryId)
void	setReadGroup(short rg)
void	setTile(short tile)
void	setX(short x)
void	setY(short y)

Methods inherited from class java.lang.Object

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

Constructor Detail

PhysicalLocationForMateCigar

public PhysicalLocationForMateCigar(OpticalDuplicateFinder.PhysicalLocation rec)

Method Detail

getReadGroup

public short getReadGroup()

Specified by:

getReadGroup in interface OpticalDuplicateFinder.PhysicalLocation

setReadGroup

public void setReadGroup(short rg)

Specified by:

setReadGroup in interface OpticalDuplicateFinder.PhysicalLocation

getTile

public short getTile()

Specified by:

getTile in interface OpticalDuplicateFinder.PhysicalLocation

setTile

public void setTile(short tile)

Specified by:

setTile in interface OpticalDuplicateFinder.PhysicalLocation

getX

public short getX()

Specified by:

getX in interface OpticalDuplicateFinder.PhysicalLocation

setX

public void setX(short x)

Specified by:

setX in interface OpticalDuplicateFinder.PhysicalLocation

getY

public short getY()

Specified by:

getY in interface OpticalDuplicateFinder.PhysicalLocation

setY

public void setY(short y)

Specified by:

setY in interface OpticalDuplicateFinder.PhysicalLocation

getLibraryId

public short getLibraryId()

Specified by:

getLibraryId in interface OpticalDuplicateFinder.PhysicalLocation

setLibraryId

public void setLibraryId(short libraryId)

Specified by:

setLibraryId in interface OpticalDuplicateFinder.PhysicalLocation

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