Package 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:
Serializable
,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.- See Also:
- Serialized Form
-
-
Field Summary
Fields Modifier and Type Field 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 matestatic 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 Description ReadEnds()
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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.
-
-
Method Detail
-
isPaired
public boolean isPaired()
-
getReadGroup
public short getReadGroup()
- Specified by:
getReadGroup
in interfacePhysicalLocation
- Overrides:
getReadGroup
in classPhysicalLocationInt
-
setReadGroup
public void setReadGroup(short readGroup)
- Specified by:
setReadGroup
in interfacePhysicalLocation
- Overrides:
setReadGroup
in classPhysicalLocationInt
-
getLibraryId
public short getLibraryId()
- Specified by:
getLibraryId
in interfacePhysicalLocation
- Overrides:
getLibraryId
in classPhysicalLocationInt
-
setLibraryId
public void setLibraryId(short libraryId)
- Specified by:
setLibraryId
in interfacePhysicalLocation
- Overrides:
setLibraryId
in classPhysicalLocationInt
-
getOrientationByte
public static byte getOrientationByte(boolean read1NegativeStrand, boolean read2NegativeStrand)
Returns a single byte that encodes the orientation of the two reads in a pair.
-
-