PhysicalLocationpublic class ReadEndsForMateCigar extends ReadEnds
| Modifier and Type | Field | Description |
|---|---|---|
htsjdk.samtools.util.SamRecordWithOrdinal |
samRecordWithOrdinal |
NO_VALUEtile, x, yF, 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, waithasLocationgetTile, getX, getY, setTilesetX, setYgetLibraryId, getOrientationByte, getReadGroup, setLibraryId, setReadGrouppublic 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)