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