picard.vcf

Class GenotypeConcordance.Alleles

java.lang.Object

picard.vcf.GenotypeConcordance.Alleles

Enclosing class:

GenotypeConcordance

protected static class GenotypeConcordance.Alleles
extends java.lang.Object

A simple structure to return the results of getAlleles. NB: truthAllele1/2 and callAllele1/2 may be null if no first or second allele was present respectively.

Field Summary

Fields

Modifier and Type	Field and Description
picard.vcf.OrderedSet<java.lang.String>	allAlleles
java.lang.String	callAllele1
java.lang.String	callAllele2
java.lang.String	truthAllele1
java.lang.String	truthAllele2

Constructor Summary

Constructors

Constructor and Description
Alleles(picard.vcf.OrderedSet<java.lang.String> allAlleles, java.lang.String truthAllele1, java.lang.String truthAllele2, java.lang.String callAllele1, java.lang.String callAllele2)

Method Summary

Modifier and Type	Method and Description
java.util.List<htsjdk.variant.variantcontext.Allele>	asList()
java.util.List<htsjdk.variant.variantcontext.Allele>	callAlleles()
java.util.List<htsjdk.variant.variantcontext.Allele>	truthAlleles()

Methods inherited from class java.lang.Object

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

Field Detail

allAlleles

public final picard.vcf.OrderedSet<java.lang.String> allAlleles

truthAllele1

public final java.lang.String truthAllele1

truthAllele2

public final java.lang.String truthAllele2

callAllele1

public final java.lang.String callAllele1

callAllele2

public final java.lang.String callAllele2

Constructor Detail

Alleles

public Alleles(picard.vcf.OrderedSet<java.lang.String> allAlleles,
               java.lang.String truthAllele1,
               java.lang.String truthAllele2,
               java.lang.String callAllele1,
               java.lang.String callAllele2)

Method Detail

asList

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

truthAlleles

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

callAlleles

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