PhysicalLocation
public class ReadEndsForMateCigar extends ReadEnds
Modifier and Type | Field | Description |
---|---|---|
htsjdk.samtools.util.SamRecordWithOrdinal |
samRecordWithOrdinal |
NO_VALUE
tile, x, y
F, FF, FR, isOpticalDuplicate, libraryId, orientation, orientationForOpticalDuplicates, R, read1Coordinate, read1ReferenceIndex, read2Coordinate, read2ReferenceIndex, readGroup, RF, RR
Constructor | Description |
---|---|
ReadEndsForMateCigar(htsjdk.samtools.SAMFileHeader header,
htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal,
OpticalDuplicateFinder opticalDuplicateFinder,
short libraryId) |
Builds a read ends object that represents a single read.
|
ReadEndsForMateCigar(ReadEndsForMateCigar other,
htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal) |
Creates a shallow copy from the "other"
|
Modifier and Type | Method | Description |
---|---|---|
PhysicalLocationForMateCigarSet |
getLocationSet() |
|
Set<ReadEnds> |
getReadEndSetForOpticalDuplicates() |
Gets the read ends for optical duplicate tracking
|
htsjdk.samtools.SAMRecord |
getRecord() |
|
String |
getRecordReadName() |
|
htsjdk.samtools.util.SamRecordWithOrdinal |
getSamRecordIndex() |
A number of convenience functions
|
boolean |
isPaired() |
|
PhysicalLocationForMateCigarSet |
removeLocationSet() |
|
void |
setLocationSet(PhysicalLocationForMateCigarSet locationSet) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
hasLocation
getTile, getX, getY, setTile
setX, setY
getLibraryId, getOrientationByte, getReadGroup, setLibraryId, setReadGroup
public htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal
public ReadEndsForMateCigar(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal, OpticalDuplicateFinder opticalDuplicateFinder, short libraryId)
public ReadEndsForMateCigar(ReadEndsForMateCigar other, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal)
public htsjdk.samtools.util.SamRecordWithOrdinal getSamRecordIndex()
public htsjdk.samtools.SAMRecord getRecord()
public String getRecordReadName()
public Set<ReadEnds> getReadEndSetForOpticalDuplicates()
public PhysicalLocationForMateCigarSet getLocationSet()
public PhysicalLocationForMateCigarSet removeLocationSet()
public void setLocationSet(PhysicalLocationForMateCigarSet locationSet)