org.broadinstitute.hellbender.tools.spark.sv.evidence

Class QNameIntervalFinder

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameIntervalFinder

All Implemented Interfaces:

java.util.function.Function<GATKRead,java.util.Iterator<QNameAndInterval>>

public final class QNameIntervalFinder
extends java.lang.Object
implements java.util.function.Function<GATKRead,java.util.Iterator<QNameAndInterval>>

Iterates over reads, kmerizing them, and checking the kmers against a set of KmerAndIntervals to figure out which intervals (if any) a read belongs in. Results are returned as a QNameAndInterval iterator.

Constructor Summary

Constructors

Constructor and Description
QNameIntervalFinder(int kSize, HopscotchUniqueMultiMap<SVKmer,java.lang.Integer,KmerAndInterval> kmerMap)

Method Summary

Modifier and Type	Method and Description
java.util.Iterator<QNameAndInterval>	apply(GATKRead read)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.function.Function

andThen, compose, identity

Constructor Detail

QNameIntervalFinder

public QNameIntervalFinder(int kSize,
                           HopscotchUniqueMultiMap<SVKmer,java.lang.Integer,KmerAndInterval> kmerMap)

Method Detail

apply

public java.util.Iterator<QNameAndInterval> apply(GATKRead read)

Specified by:

apply in interface java.util.function.Function<GATKRead,java.util.Iterator<QNameAndInterval>>