public abstract class ReadEnds extends PhysicalLocationShort
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 |
tile, x, y
NO_VALUE
Constructor and Description |
---|
ReadEnds() |
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) |
setX, setY
getTile, getX, getY, setTile
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
hasLocation
public static final byte F
public static final byte R
public static final byte FF
public static final byte FR
public static final byte RR
public static final byte RF
public short libraryId
public byte orientation
public int read1ReferenceIndex
public int read1Coordinate
public int read2ReferenceIndex
public int read2Coordinate
public short readGroup
public byte orientationForOpticalDuplicates
public transient boolean isOpticalDuplicate
public boolean isPaired()
public short getReadGroup()
getReadGroup
in interface PhysicalLocation
getReadGroup
in class PhysicalLocationInt
public void setReadGroup(short readGroup)
setReadGroup
in interface PhysicalLocation
setReadGroup
in class PhysicalLocationInt
public short getLibraryId()
getLibraryId
in interface PhysicalLocation
getLibraryId
in class PhysicalLocationInt
public void setLibraryId(short libraryId)
setLibraryId
in interface PhysicalLocation
setLibraryId
in class PhysicalLocationInt
public static byte getOrientationByte(boolean read1NegativeStrand, boolean read2NegativeStrand)