picard.sam.markduplicates.util

Class ReadEnds

java.lang.Object

picard.sam.util.PhysicalLocationInt

picard.sam.util.PhysicalLocationShort

picard.sam.markduplicates.util.ReadEnds

All Implemented Interfaces:

PhysicalLocation

Direct Known Subclasses:

ReadEndsForMarkDuplicates, ReadEndsForMateCigar

public abstract class ReadEnds
extends PhysicalLocationShort

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
boolean	isOpticalDuplicate A *transient* flag marking this read end as being an optical duplicate.
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

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
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()
boolean	isPaired()
void	setLibraryId(short libraryId)
void	setReadGroup(short readGroup)

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

Methods inherited from interface picard.sam.util.PhysicalLocation

hasLocation

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

orientationForOpticalDuplicates

public byte orientationForOpticalDuplicates

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

isOpticalDuplicate

public transient boolean isOpticalDuplicate

A *transient* flag marking this read end as being an optical duplicate.

Constructor Detail

ReadEnds

public ReadEnds()

Method Detail

isPaired

public boolean isPaired()

getReadGroup

public short getReadGroup()

Specified by:

getReadGroup in interface PhysicalLocation

Overrides:

getReadGroup in class PhysicalLocationInt

setReadGroup

public void setReadGroup(short readGroup)

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

getOrientationByte

public static byte getOrientationByte(boolean read1NegativeStrand,
                                      boolean read2NegativeStrand)

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