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.
-
-
Field Summary
Fields Modifier and Type Field Description String
CALL_SAMPLE
The name of the 'call' samplelong
EMPTY_COUNT
The empty (no contingency info) count across all variantslong
FN_COUNT
The FN (false negative) count across all variantslong
FP_COUNT
The FP (false positive) count across all variantslong
TN_COUNT
The TN (true negative) count across all variantslong
TP_COUNT
The TP (true positive) count across all variantsString
TRUTH_SAMPLE
The name of the 'truth' samplehtsjdk.variant.variantcontext.VariantContext.Type
VARIANT_TYPE
The type of the event (i.e.
-
Constructor Summary
Constructors Constructor Description GenotypeConcordanceContingencyMetrics()
Empty constructor - needed for unit testsGenotypeConcordanceContingencyMetrics(htsjdk.variant.variantcontext.VariantContext.Type variantType, GenotypeConcordanceCounts concordanceCounts, String truthSample, String callSample, boolean missingSitesFlag)
-
-
-
Field Detail
-
VARIANT_TYPE
public htsjdk.variant.variantcontext.VariantContext.Type VARIANT_TYPE
The type of the event (i.e. either SNP or INDEL)
-
TRUTH_SAMPLE
public String TRUTH_SAMPLE
The name of the 'truth' sample
-
CALL_SAMPLE
public String CALL_SAMPLE
The name of the 'call' sample
-
TP_COUNT
public long TP_COUNT
The TP (true positive) count across all variants
-
TN_COUNT
public long TN_COUNT
The TN (true negative) count across all variants
-
FP_COUNT
public long FP_COUNT
The FP (false positive) count across all variants
-
FN_COUNT
public long FN_COUNT
The FN (false negative) count across all variants
-
EMPTY_COUNT
public long EMPTY_COUNT
The empty (no contingency info) count across all variants
-
-
Constructor Detail
-
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)
-
-