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