picard.vcf

Class GenotypeConcordanceStates

java.lang.Object

picard.vcf.GenotypeConcordanceStates

public class GenotypeConcordanceStates
extends java.lang.Object

A class to store the various classifications for: 1. a truth genotype versus a reference 2. a call genotype versus a truth, relative to a reference An example use of this class is to have one instance per following use case: - SNPs - indels - filtered variant (truth or call) - filtered genotype (truth or call) - low GQ (call) - low DP (call) - No call (truth or call) - No variant (truth or call) *

Author:

nhomer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GenotypeConcordanceStates.CallState These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence.
static class	GenotypeConcordanceStates.ContingencyState A specific state for a 2x2 contingency table.
static class	GenotypeConcordanceStates.TruthAndCallStates A minute class to store the truth and call state respectively.
static class	GenotypeConcordanceStates.TruthState These states represent the relationship between a truth genotype and the reference sequence.

Constructor Summary

Constructors

Constructor and Description
GenotypeConcordanceStates()

Method Summary

Methods inherited from class java.lang.Object

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

Constructor Detail

GenotypeConcordanceStates

public GenotypeConcordanceStates()