picard.sam.markduplicates.util

Class ReadEnds

java.lang.Object

picard.sam.markduplicates.util.ReadEnds

All Implemented Interfaces:

OpticalDuplicateFinder.PhysicalLocation

Direct Known Subclasses:

ReadEndsForMarkDuplicates, ReadEndsForMateCigar

public abstract class ReadEnds
extends java.lang.Object
implements OpticalDuplicateFinder.PhysicalLocation

Little struct-like class to hold read pair (and fragment) end data for duplicate marking.

Field Summary

Fields

Modifier and Type	Field and Description
static byte	F
static byte	FF
static byte	FR
short	libraryId
byte	orientation
byte	orientationForOpticalDuplicates For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate
static byte	R
int	read1Coordinate
int	read1ReferenceIndex
int	read2Coordinate
int	read2ReferenceIndex
short	readGroup
static byte	RF
static byte	RR
short	tile
short	x
short	y

Constructor Summary

Constructors

Constructor and Description
ReadEnds()

Method Summary

Modifier and Type	Method and Description
short	getLibraryId()
static byte	getOrientationByte(boolean read1NegativeStrand, boolean read2NegativeStrand) Returns a single byte that encodes the orientation of the two reads in a pair.
short	getReadGroup()
short	getTile()
short	getX()
short	getY()
boolean	isPaired()
void	setLibraryId(short libraryId)
void	setReadGroup(short readGroup)
void	setTile(short tile)
void	setX(short x)
void	setY(short y)

Methods inherited from class java.lang.Object

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

Field Detail

F

public static final byte F

See Also:

Constant Field Values

R

public static final byte R

See Also:

Constant Field Values

FF

public static final byte FF

See Also:

Constant Field Values

FR

public static final byte FR

See Also:

Constant Field Values

RR

public static final byte RR

See Also:

Constant Field Values

RF

public static final byte RF

See Also:

Constant Field Values

libraryId

public short libraryId

orientation

public byte orientation

read1ReferenceIndex

public int read1ReferenceIndex

read1Coordinate

public int read1Coordinate

read2ReferenceIndex

public int read2ReferenceIndex

read2Coordinate

public int read2Coordinate

readGroup

public short readGroup

tile

public short tile

x

public short x

y

public short y

orientationForOpticalDuplicates

public byte orientationForOpticalDuplicates

For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate

Constructor Detail

ReadEnds

public ReadEnds()

Method Detail

isPaired

public boolean isPaired()

getReadGroup

public short getReadGroup()

Specified by:

getReadGroup in interface OpticalDuplicateFinder.PhysicalLocation

setReadGroup

public void setReadGroup(short readGroup)

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

getOrientationByte

public static byte getOrientationByte(boolean read1NegativeStrand,
                                      boolean read2NegativeStrand)

Returns a single byte that encodes the orientation of the two reads in a pair.