org.broadinstitute.hellbender.engine

Class AbstractConcordanceWalker.TruthVersusEval

java.lang.Object

org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval

All Implemented Interfaces:

htsjdk.samtools.util.Locatable

Enclosing class:

AbstractConcordanceWalker

protected static class AbstractConcordanceWalker.TruthVersusEval
extends java.lang.Object
implements htsjdk.samtools.util.Locatable

store a truth vc in case of a false negative, an eval vc in case of a false positive, or a concordance pair of truth and eval in case of a true positive.

Method Summary

Modifier and Type	Method and Description
static AbstractConcordanceWalker.TruthVersusEval	falseNegative(htsjdk.variant.variantcontext.VariantContext truth)
static AbstractConcordanceWalker.TruthVersusEval	falsePositive(htsjdk.variant.variantcontext.VariantContext eval)
static AbstractConcordanceWalker.TruthVersusEval	filteredFalseNegative(htsjdk.variant.variantcontext.VariantContext truth, htsjdk.variant.variantcontext.VariantContext eval)
static AbstractConcordanceWalker.TruthVersusEval	filteredTrueNegative(htsjdk.variant.variantcontext.VariantContext eval)
ConcordanceState	getConcordance()
java.lang.String	getContig()
int	getEnd()
htsjdk.variant.variantcontext.VariantContext	getEval()
int	getStart()
htsjdk.variant.variantcontext.VariantContext	getTruth()
htsjdk.variant.variantcontext.VariantContext	getTruthIfPresentElseEval()
boolean	hasEval()
boolean	hasTruth()
static AbstractConcordanceWalker.TruthVersusEval	truePositive(htsjdk.variant.variantcontext.VariantContext truth, htsjdk.variant.variantcontext.VariantContext eval)

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Method Detail

falseNegative

public static AbstractConcordanceWalker.TruthVersusEval falseNegative(htsjdk.variant.variantcontext.VariantContext truth)

falsePositive

public static AbstractConcordanceWalker.TruthVersusEval falsePositive(htsjdk.variant.variantcontext.VariantContext eval)

truePositive

public static AbstractConcordanceWalker.TruthVersusEval truePositive(htsjdk.variant.variantcontext.VariantContext truth,
                                                                     htsjdk.variant.variantcontext.VariantContext eval)

filteredFalseNegative

public static AbstractConcordanceWalker.TruthVersusEval filteredFalseNegative(htsjdk.variant.variantcontext.VariantContext truth,
                                                                              htsjdk.variant.variantcontext.VariantContext eval)

filteredTrueNegative

public static AbstractConcordanceWalker.TruthVersusEval filteredTrueNegative(htsjdk.variant.variantcontext.VariantContext eval)

getConcordance

public ConcordanceState getConcordance()

getTruth

public htsjdk.variant.variantcontext.VariantContext getTruth()

getEval

public htsjdk.variant.variantcontext.VariantContext getEval()

hasTruth

public boolean hasTruth()

hasEval

public boolean hasEval()

getTruthIfPresentElseEval

public htsjdk.variant.variantcontext.VariantContext getTruthIfPresentElseEval()

getContig

public java.lang.String getContig()

Specified by:

getContig in interface htsjdk.samtools.util.Locatable

getStart

public int getStart()

Specified by:

getStart in interface htsjdk.samtools.util.Locatable

getEnd

public int getEnd()

Specified by:

getEnd in interface htsjdk.samtools.util.Locatable