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

Class KmerCounter

java.lang.Object

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

public final class KmerCounter
extends java.lang.Object

Iterates over reads, kmerizing them, and counting up just the kmers that appear in a passed-in set. The counts are returned as a KmerAndCount iterator.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
java.util.Iterator<KmerAndCount>	apply(java.util.Iterator<GATKRead> readItr)

Methods inherited from class java.lang.Object

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

Constructor Detail

KmerCounter

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

Method Detail

apply

public java.util.Iterator<KmerAndCount> apply(java.util.Iterator<GATKRead> readItr)