Uses of Class
picard.vcf.GenotypeConcordanceScheme

Packages that use GenotypeConcordanceScheme

Package	Description
picard.vcf

Uses of GenotypeConcordanceScheme in picard.vcf

Subclasses of GenotypeConcordanceScheme in picard.vcf

Modifier and Type	Class and Description
class	GA4GHScheme The scheme is defined in the constructor.
class	GA4GHSchemeWithMissingAsHomRef The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.

Methods in picard.vcf that return GenotypeConcordanceScheme

Modifier and Type	Method and Description
GenotypeConcordanceScheme	GenotypeConcordanceSchemeFactory.getScheme(boolean isMissingHomRef)

Methods in picard.vcf with parameters of type GenotypeConcordanceScheme

Modifier and Type	Method and Description
double	GenotypeConcordanceCounts.calculateGenotypeConcordance(GenotypeConcordanceScheme scheme, boolean missingSitesFlag) Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
double	GenotypeConcordanceCounts.calculateNonRefGenotypeConcordance(GenotypeConcordanceScheme scheme, boolean missingSitesFlag) Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
java.util.Map<GenotypeConcordanceStates.ContingencyState,java.lang.Long>	GenotypeConcordanceCounts.getContingencyStateCounts(GenotypeConcordanceScheme scheme) Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
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.
double	GenotypeConcordanceCounts.Ppv(GenotypeConcordanceScheme scheme, GenotypeConcordanceStates.CallState[] callStateList) Returns the PPV defined by the scheme across the subset of call states.
void	GenotypeConcordanceCounts.validateCountsAgainstScheme(GenotypeConcordanceScheme scheme) Validates that there are no counts for NA states in the underlying scheme