org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords

Class PairedEnds

java.lang.Object

org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord

org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.PairedEnds

Direct Known Subclasses:

EmptyFragment, Fragment, Pair

public abstract class PairedEnds
extends MarkDuplicatesSparkRecord

Struct-like class to store information about the paired reads for mark duplicates.

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord

MarkDuplicatesSparkRecord.Type

Field Summary

Fields inherited from class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord

name, partitionIndex

Method Summary

Modifier and Type	Method and Description
abstract int	getFirstRefIndex()
abstract int	getFirstStartPosition()
abstract byte	getOrientationForPCRDuplicates() This returns a byte summary spanning from 0-5 representing all combinations of single read or two read forward/reverse strand for the first and second read in the Pair.
abstract int	getScore()
abstract int	getUnclippedStartPosition()
abstract boolean	isRead1ReverseStrand()

Methods inherited from class org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord

getName, getPartitionIndex, getPassthrough, getType, key, newEmptyFragment, newFragment, newPair

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getFirstStartPosition

public abstract int getFirstStartPosition()

getUnclippedStartPosition

public abstract int getUnclippedStartPosition()

getFirstRefIndex

public abstract int getFirstRefIndex()

getScore

public abstract int getScore()

isRead1ReverseStrand

public abstract boolean isRead1ReverseStrand()

getOrientationForPCRDuplicates

public abstract byte getOrientationForPCRDuplicates()

This returns a byte summary spanning from 0-5 representing all combinations of single read or two read forward/reverse strand for the first and second read in the Pair. Note, for PCR Duplicates orientation that the 'first' read corresponds to the read that appears first by coordinate sorting order, which is distinct from optical sorting which considers the 'first' read to be the first in pair.