org.disq_bio.disq

Class HtsjdkReadsTraversalParameters<T extends htsjdk.samtools.util.Locatable>

java.lang.Object

org.disq_bio.disq.HtsjdkReadsTraversalParameters<T>

Type Parameters:

T - the type of Locatable

public class HtsjdkReadsTraversalParameters<T extends htsjdk.samtools.util.Locatable>
extends Object

Holds parameters controlling which reads get returned when reading a HtsjdkReadsRdd. Parameters include the intervals to include, and a flag controlling whether unplaced, unmapped reads should be returned.

Constructor Summary

Constructors

Constructor and Description
HtsjdkReadsTraversalParameters(List<T> intervalsForTraversal, boolean traverseUnplacedUnmapped)

Method Summary

Modifier and Type	Method and Description
List<T>	getIntervalsForTraversal()
boolean	getTraverseUnplacedUnmapped()

Methods inherited from class java.lang.Object

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

Constructor Detail

HtsjdkReadsTraversalParameters

public HtsjdkReadsTraversalParameters(List<T> intervalsForTraversal,
                                      boolean traverseUnplacedUnmapped)

Method Detail

getIntervalsForTraversal

public List<T> getIntervalsForTraversal()

getTraverseUnplacedUnmapped

public boolean getTraverseUnplacedUnmapped()