Package picard.vcf
Class GenotypeConcordanceContingencyMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.vcf.GenotypeConcordanceContingencyMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class GenotypeConcordanceContingencyMetrics
extends htsjdk.samtools.metrics.MetricBase
Class that holds metrics about the Genotype Concordance contingency tables.
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Field Summary
FieldsModifier and TypeFieldDescriptionThe name of the 'call' samplelong
The empty (no contingency info) count across all variantslong
The FN (false negative) count across all variantslong
The FP (false positive) count across all variantslong
The TN (true negative) count across all variantslong
The TP (true positive) count across all variantsThe name of the 'truth' samplehtsjdk.variant.variantcontext.VariantContext.Type
The type of the event (i.e. -
Constructor Summary
ConstructorsConstructorDescriptionEmpty constructor - needed for unit testsGenotypeConcordanceContingencyMetrics
(htsjdk.variant.variantcontext.VariantContext.Type variantType, GenotypeConcordanceCounts concordanceCounts, String truthSample, String callSample, boolean missingSitesFlag) -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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VARIANT_TYPE
public htsjdk.variant.variantcontext.VariantContext.Type VARIANT_TYPEThe type of the event (i.e. either SNP or INDEL) -
TRUTH_SAMPLE
The name of the 'truth' sample -
CALL_SAMPLE
The name of the 'call' sample -
TP_COUNT
public long TP_COUNTThe TP (true positive) count across all variants -
TN_COUNT
public long TN_COUNTThe TN (true negative) count across all variants -
FP_COUNT
public long FP_COUNTThe FP (false positive) count across all variants -
FN_COUNT
public long FN_COUNTThe FN (false negative) count across all variants -
EMPTY_COUNT
public long EMPTY_COUNTThe empty (no contingency info) count across all variants
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Constructor Details
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GenotypeConcordanceContingencyMetrics
public GenotypeConcordanceContingencyMetrics()Empty constructor - needed for unit tests -
GenotypeConcordanceContingencyMetrics
public GenotypeConcordanceContingencyMetrics(htsjdk.variant.variantcontext.VariantContext.Type variantType, GenotypeConcordanceCounts concordanceCounts, String truthSample, String callSample, boolean missingSitesFlag)
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