picard.sam.markduplicates.util

Interface OpticalDuplicateFinder.PhysicalLocation

All Known Implementing Classes:

PhysicalLocationForMateCigar, ReadEnds, ReadEndsForMarkDuplicates, ReadEndsForMarkDuplicatesWithBarcodes, ReadEndsForMateCigar

Enclosing class:

OpticalDuplicateFinder

public static interface OpticalDuplicateFinder.PhysicalLocation

Small interface that provides access to the physical location information about a cluster. All values should be defaulted to -1 if unavailable. ReadGroup and Tile should only allow non-zero positive integers, x and y coordinates may be negative.

Method Summary

Modifier and Type	Method and Description
short	getLibraryId()
short	getReadGroup()
short	getTile()
short	getX()
short	getY()
void	setLibraryId(short libraryId)
void	setReadGroup(short rg)
void	setTile(short tile)
void	setX(short x)
void	setY(short y)

Method Detail

getReadGroup

short getReadGroup()

setReadGroup

void setReadGroup(short rg)

getTile

short getTile()

setTile

void setTile(short tile)

getX

short getX()

setX

void setX(short x)

getY

short getY()

setY

void setY(short y)

getLibraryId

short getLibraryId()

setLibraryId

void setLibraryId(short libraryId)