Uses of Class
picard.vcf.GenotypeConcordanceStates.TruthState

Packages that use GenotypeConcordanceStates.TruthState

Package	Description
picard.vcf

Uses of GenotypeConcordanceStates.TruthState in picard.vcf

Fields in picard.vcf declared as GenotypeConcordanceStates.TruthState

Modifier and Type	Field and Description
GenotypeConcordanceStates.TruthState	GenotypeConcordanceDetailMetrics.TRUTH_STATE The state of the 'truth' sample (i.e.
GenotypeConcordanceStates.TruthState	GenotypeConcordanceStates.TruthAndCallStates.truthState

Methods in picard.vcf that return GenotypeConcordanceStates.TruthState

Modifier and Type	Method and Description
static GenotypeConcordanceStates.TruthState	GenotypeConcordanceStates.TruthState.getHom(int alleleIdx)
static GenotypeConcordanceStates.TruthState	GenotypeConcordanceStates.TruthState.getVar(int allele0idx, int allele1idx)
static GenotypeConcordanceStates.TruthState	GenotypeConcordanceStates.TruthState.valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static GenotypeConcordanceStates.TruthState[]	GenotypeConcordanceStates.TruthState.values() Returns an array containing the constants of this enum type, in the order they are declared.

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

Modifier and Type	Method and Description
GenotypeConcordanceStates.ContingencyState[]	GenotypeConcordanceScheme.getConcordanceStateArray(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState) Get the concordance state array associate with the given truth state and call state tuple.
java.lang.String	GenotypeConcordanceScheme.getContingencyStateString(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState) Get the contingency state array as a parse-able string
long	GenotypeConcordanceCounts.getCount(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState) Returns the count defined by the truth state set and call state set.
double	GenotypeConcordanceCounts.getSensitivity(GenotypeConcordanceScheme scheme, GenotypeConcordanceStates.TruthState[] truthStateArray) Returns the sensitivity defined by the scheme across the subset of truth states.
double	GenotypeConcordanceCounts.getSpecificity(GenotypeConcordanceScheme scheme, GenotypeConcordanceStates.TruthState[] truthStateArray) Returns the specificity defined by the scheme across the subset of truth states.
boolean	GenotypeConcordanceCounts.isMissing(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState) Returns true if EITHER the truth or call state is MISSING.
boolean	GenotypeConcordanceCounts.isVar(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState) Returns true if EITHER the truth or call state is a VAR.

Method parameters in picard.vcf with type arguments of type GenotypeConcordanceStates.TruthState

Modifier and Type	Method and Description
long	GenotypeConcordanceCounts.getSum(java.util.Set<GenotypeConcordanceStates.TruthState> truthStateSet, java.util.Set<GenotypeConcordanceStates.CallState> callStateSet) Returns the sum of all pairs of tuples defined by the truth state set and call state set.

Constructors in picard.vcf with parameters of type GenotypeConcordanceStates.TruthState

Constructor and Description
TruthAndCallStates(GenotypeConcordanceStates.TruthState truthState, GenotypeConcordanceStates.CallState callState)