Package picard.vcf

Class GenotypeConcordanceContingencyMetrics


  • public class GenotypeConcordanceContingencyMetrics
    extends htsjdk.samtools.metrics.MetricBase
    Class that holds metrics about the Genotype Concordance contingency tables.
    • 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)