Uses of Class
picard.vcf.GenotypeConcordanceCounts

Packages that use GenotypeConcordanceCounts

Package	Description
picard.vcf

Uses of GenotypeConcordanceCounts in picard.vcf

Fields in picard.vcf declared as GenotypeConcordanceCounts

Modifier and Type	Field and Description
protected GenotypeConcordanceCounts	GenotypeConcordance.indelCounter
protected GenotypeConcordanceCounts	GenotypeConcordance.snpCounter

Methods in picard.vcf that return GenotypeConcordanceCounts

Modifier and Type	Method and Description
GenotypeConcordanceCounts	GenotypeConcordance.getIndelCounter()
GenotypeConcordanceCounts	GenotypeConcordance.getSnpCounter()

Methods in picard.vcf with parameters of type GenotypeConcordanceCounts

Modifier and Type	Method and Description
static void	GenotypeConcordance.addMissingTruthAndMissingCallStates(double numVariants, long intervalBaseCount, GenotypeConcordanceCounts counter) Method to add missing sites that are KNOWN to be HOM_REF in the case of the NIST truth data set.
static void	GenotypeConcordance.outputDetailMetricsFile(htsjdk.variant.variantcontext.VariantContext.Type variantType, htsjdk.samtools.metrics.MetricsFile<GenotypeConcordanceDetailMetrics,?> genotypeConcordanceDetailMetricsFile, GenotypeConcordanceCounts counter, java.lang.String truthSampleName, java.lang.String callSampleName, boolean missingSitesHomRef, boolean outputAllRows) Outputs the detailed statistics tables for SNP and Indel match categories.

Method parameters in picard.vcf with type arguments of type GenotypeConcordanceCounts

Modifier and Type	Method and Description
static boolean	GenotypeConcordance.classifyVariants(java.util.Optional<htsjdk.variant.variantcontext.VariantContext> truthContext, java.lang.String truthSample, java.util.Optional<htsjdk.variant.variantcontext.VariantContext> callContext, java.lang.String callSample, java.util.Optional<GenotypeConcordanceCounts> snpCounter, java.util.Optional<GenotypeConcordanceCounts> indelCounter, int minGq, int minDp) Attempts to determine the concordance state given the truth and all variant context and optionally increments the genotype concordance count for the given variant type (SNP or INDEL).
static boolean	GenotypeConcordance.classifyVariants(java.util.Optional<htsjdk.variant.variantcontext.VariantContext> truthContext, java.lang.String truthSample, java.util.Optional<htsjdk.variant.variantcontext.VariantContext> callContext, java.lang.String callSample, java.util.Optional<GenotypeConcordanceCounts> snpCounter, java.util.Optional<GenotypeConcordanceCounts> indelCounter, int minGq, int minDp) Attempts to determine the concordance state given the truth and all variant context and optionally increments the genotype concordance count for the given variant type (SNP or INDEL).

Constructors in picard.vcf with parameters of type GenotypeConcordanceCounts

Constructor and Description
GenotypeConcordanceContingencyMetrics(htsjdk.variant.variantcontext.VariantContext.Type variantType, GenotypeConcordanceCounts concordanceCounts, java.lang.String truthSample, java.lang.String callSample, boolean missingSitesFlag)
GenotypeConcordanceSummaryMetrics(htsjdk.variant.variantcontext.VariantContext.Type variantType, GenotypeConcordanceCounts concordanceCounts, java.lang.String truthSample, java.lang.String callSample, boolean missingSitesFlag)