org.broadinstitute.hellbender.tools.spark.sv.utils

Class KmerAndCount

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer

org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong

org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount

All Implemented Interfaces:

java.lang.Comparable<SVKmerLong>, java.util.Map.Entry<SVKmer,java.lang.Integer>

public final class KmerAndCount
extends SVKmerLong
implements java.util.Map.Entry<SVKmer,java.lang.Integer>

A pair.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	KmerAndCount.Serializer

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer

SVKmer.Base

Field Summary

Fields inherited from class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer

BYTEWISE_REVERSE_COMPLEMENT

Constructor Summary

Constructors

Constructor and Description
KmerAndCount(SVKmerLong kmer)
KmerAndCount(SVKmerLong kmer, int count)

Method Summary

Modifier and Type	Method and Description
void	bumpCount()
void	bumpCount(int extra)
SVKmer	getKey()
java.lang.Integer	getValue()
int	grabCount()
protected void	serialize(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Output output)
java.lang.Integer	setValue(java.lang.Integer count)

Methods inherited from class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong

canonical, compareTo, equals, equals, firstBase, firstTrimer, hashCode, lastBase, lastTrimer, predecessor, reverseComplement, successor, toString

Methods inherited from class org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer

reverseComplement, reverseComplementByteValueAsLong

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Map.Entry

comparingByKey, comparingByKey, comparingByValue, comparingByValue, equals, hashCode

Constructor Detail

KmerAndCount

public KmerAndCount(SVKmerLong kmer)

KmerAndCount

public KmerAndCount(SVKmerLong kmer,
                    int count)

Method Detail

serialize

protected void serialize(com.esotericsoftware.kryo.Kryo kryo,
                         com.esotericsoftware.kryo.io.Output output)

Overrides:

serialize in class SVKmerLong

getKey

public SVKmer getKey()

Specified by:

getKey in interface java.util.Map.Entry<SVKmer,java.lang.Integer>

getValue

public java.lang.Integer getValue()

Specified by:

getValue in interface java.util.Map.Entry<SVKmer,java.lang.Integer>

setValue

public java.lang.Integer setValue(java.lang.Integer count)

Specified by:

setValue in interface java.util.Map.Entry<SVKmer,java.lang.Integer>

grabCount

public int grabCount()

bumpCount

public void bumpCount()

bumpCount

public void bumpCount(int extra)