org.broadinstitute.hellbender.utils.variant

Class GATKVariantContextUtils.AlleleMapper

java.lang.Object

org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.AlleleMapper

Enclosing class:

GATKVariantContextUtils

protected static class GATKVariantContextUtils.AlleleMapper
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
AlleleMapper(java.util.Map<htsjdk.variant.variantcontext.Allele,htsjdk.variant.variantcontext.Allele> map)
AlleleMapper(htsjdk.variant.variantcontext.VariantContext vc)

Method Summary

Modifier and Type	Method and Description
boolean	needsRemapping()
htsjdk.variant.variantcontext.Allele	remap(htsjdk.variant.variantcontext.Allele a)
java.util.List<htsjdk.variant.variantcontext.Allele>	remap(java.util.List<htsjdk.variant.variantcontext.Allele> as)
java.util.Collection<htsjdk.variant.variantcontext.Allele>	values()

Methods inherited from class java.lang.Object

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

Constructor Detail

AlleleMapper

public AlleleMapper(htsjdk.variant.variantcontext.VariantContext vc)

AlleleMapper

public AlleleMapper(java.util.Map<htsjdk.variant.variantcontext.Allele,htsjdk.variant.variantcontext.Allele> map)

Method Detail

needsRemapping

public boolean needsRemapping()

values

public java.util.Collection<htsjdk.variant.variantcontext.Allele> values()

remap

public htsjdk.variant.variantcontext.Allele remap(htsjdk.variant.variantcontext.Allele a)

remap

public java.util.List<htsjdk.variant.variantcontext.Allele> remap(java.util.List<htsjdk.variant.variantcontext.Allele> as)