Uses of Class
picard.vcf.GenotypeConcordanceStates.TruthAndCallStates

Packages that use GenotypeConcordanceStates.TruthAndCallStates

Package	Description
picard.vcf

Uses of GenotypeConcordanceStates.TruthAndCallStates in picard.vcf

Fields in picard.vcf with type parameters of type GenotypeConcordanceStates.TruthAndCallStates

Modifier and Type	Field and Description
protected java.util.Map<GenotypeConcordanceStates.TruthAndCallStates,GenotypeConcordanceStates.ContingencyState[]>	GenotypeConcordanceScheme.scheme The underlying scheme

Methods in picard.vcf that return GenotypeConcordanceStates.TruthAndCallStates

Modifier and Type	Method and Description
static GenotypeConcordanceStates.TruthAndCallStates	GenotypeConcordance.determineState(htsjdk.variant.variantcontext.VariantContext truthContext, java.lang.String truthSample, htsjdk.variant.variantcontext.VariantContext callContext, java.lang.String callSample, int minGq, int minDp) A method to determine the truth and call states for a pair of variant contexts representing truth and call.

Methods in picard.vcf with parameters of type GenotypeConcordanceStates.TruthAndCallStates

Modifier and Type	Method and Description
int	GenotypeConcordanceStates.TruthAndCallStates.compareTo(GenotypeConcordanceStates.TruthAndCallStates that)
GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates) Get the concordance state array associate with the given truth state and call state tuple.
long	GenotypeConcordanceCounts.getCount(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates) Returns the count defined by the truth state set and call state set.
void	GenotypeConcordanceCounts.increment(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates) Increments a count for the truth/call state tuple.
void	GenotypeConcordanceCounts.increment(GenotypeConcordanceStates.TruthAndCallStates truthAndCallStates, double count)