public abstract class ReadEnds extends Object implements OpticalDuplicateFinder.PhysicalLocation
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 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() |
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) |
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 short tile
public short x
public short y
public byte orientationForOpticalDuplicates
public boolean isPaired()
public short getReadGroup()
getReadGroup
in interface OpticalDuplicateFinder.PhysicalLocation
public void setReadGroup(short readGroup)
setReadGroup
in interface OpticalDuplicateFinder.PhysicalLocation
public short getTile()
getTile
in interface OpticalDuplicateFinder.PhysicalLocation
public void setTile(short tile)
setTile
in interface OpticalDuplicateFinder.PhysicalLocation
public short getX()
getX
in interface OpticalDuplicateFinder.PhysicalLocation
public void setX(short x)
setX
in interface OpticalDuplicateFinder.PhysicalLocation
public short getY()
getY
in interface OpticalDuplicateFinder.PhysicalLocation
public void setY(short y)
setY
in interface OpticalDuplicateFinder.PhysicalLocation
public short getLibraryId()
getLibraryId
in interface OpticalDuplicateFinder.PhysicalLocation
public void setLibraryId(short libraryId)
setLibraryId
in interface OpticalDuplicateFinder.PhysicalLocation
public static byte getOrientationByte(boolean read1NegativeStrand, boolean read2NegativeStrand)