org.broadinstitute.hellbender.tools.walkers.mutect

Class PerAlleleCollection<X extends java.lang.Number>

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection<X>

public class PerAlleleCollection<X extends java.lang.Number>
extends java.lang.Object

A container for allele to value mapping. Each PerAlleleCollection may hold a value for each ALT allele and, optionally, a value for the REF allele. For example, PerAlleleCollection alleleFractions = PerAlleleCollection.createPerAltAlleleCollection() may be a container for allele fractions for ALT alleles in a variant context. While PerAlleleCollection alleleCount = PerAlleleCollection.createPerRefAndAltAlleleCollection() may hold the allele counts for the REF allele and all ALT alleles in a variant context.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PerAlleleCollection.Type

Constructor Summary

Constructors

Constructor and Description
PerAlleleCollection(PerAlleleCollection.Type type)

Method Summary

Modifier and Type	Method and Description
double[]	asDoubleArray(java.util.Collection<htsjdk.variant.variantcontext.Allele> allelesInOrder)
X	get(htsjdk.variant.variantcontext.Allele allele) Get the value for an allele, REF or ALT
X	getAlt(htsjdk.variant.variantcontext.Allele allele)
java.util.Set<htsjdk.variant.variantcontext.Allele>	getAltAlleles()
X	getRef()
htsjdk.variant.variantcontext.Allele	getRefAllele()
void	set(htsjdk.variant.variantcontext.Allele allele, X value) Take an allele, REF or ALT, and update its value appropriately
void	set(java.util.Collection<htsjdk.variant.variantcontext.Allele> alleles, java.util.function.Function<htsjdk.variant.variantcontext.Allele,X> function)
void	setAlt(htsjdk.variant.variantcontext.Allele allele, X value)
void	setRef(htsjdk.variant.variantcontext.Allele allele, X value)

Methods inherited from class java.lang.Object

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

Constructor Detail

PerAlleleCollection

public PerAlleleCollection(PerAlleleCollection.Type type)

Method Detail

set

public void set(htsjdk.variant.variantcontext.Allele allele,
                X value)

Take an allele, REF or ALT, and update its value appropriately

Parameters:

allele - : REF or ALT allele

value - :

set

public void set(java.util.Collection<htsjdk.variant.variantcontext.Allele> alleles,
                java.util.function.Function<htsjdk.variant.variantcontext.Allele,X> function)

setRef

public void setRef(htsjdk.variant.variantcontext.Allele allele,
                   X value)

setAlt

public void setAlt(htsjdk.variant.variantcontext.Allele allele,
                   X value)

get

public X get(htsjdk.variant.variantcontext.Allele allele)

Get the value for an allele, REF or ALT

Parameters:

allele -

getRef

public X getRef()

getAlt

public X getAlt(htsjdk.variant.variantcontext.Allele allele)

asDoubleArray

public double[] asDoubleArray(java.util.Collection<htsjdk.variant.variantcontext.Allele> allelesInOrder)

getAltAlleles

public java.util.Set<htsjdk.variant.variantcontext.Allele> getAltAlleles()

getRefAllele

public htsjdk.variant.variantcontext.Allele getRefAllele()