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 Details

    • 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 Details

    • 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)