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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
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package picard.vcf;

import htsjdk.samtools.metrics.MetricBase;
import htsjdk.variant.variantcontext.VariantContext;

/**
 * Class that holds summary metrics about Genotype Concordance
 *
 * @author George Grant
 */
public class GenotypeConcordanceSummaryMetrics extends MetricBase {
    /**
     * Empty constructor - needed for unit tests
     */
    public GenotypeConcordanceSummaryMetrics() {
    }

    public GenotypeConcordanceSummaryMetrics(final VariantContext.Type variantType, final GenotypeConcordanceCounts concordanceCounts,
                                      final String truthSample, final String callSample, final boolean missingSitesFlag) {
        this.VARIANT_TYPE = variantType;
        this.TRUTH_SAMPLE = truthSample;
        this.CALL_SAMPLE = callSample;

        final GenotypeConcordanceSchemeFactory schemeFactory = new GenotypeConcordanceSchemeFactory();
        final GenotypeConcordanceScheme scheme = schemeFactory.getScheme(missingSitesFlag);
        scheme.validateScheme();
        concordanceCounts.validateCountsAgainstScheme(scheme);

        this.HET_SENSITIVITY = concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.HET_TRUTH_STATES);
        this.HET_PPV = concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.HET_CALL_STATES);
        this.HET_SPECIFICITY = Double.NaN;

        this.HOMVAR_SENSITIVITY = concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.HOM_VAR_TRUTH_STATES);
        this.HOMVAR_PPV = concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.HOM_VAR_CALL_STATES);
        this.HOMVAR_SPECIFICITY = Double.NaN;

        this.VAR_SENSITIVITY = concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.VAR_TRUTH_STATES);
        this.VAR_PPV = concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.VAR_CALL_STATES);
        this.VAR_SPECIFICITY = concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.VAR_TRUTH_STATES);

        this.GENOTYPE_CONCORDANCE = concordanceCounts.calculateGenotypeConcordance(scheme, missingSitesFlag);
        this.NON_REF_GENOTYPE_CONCORDANCE = concordanceCounts.calculateNonRefGenotypeConcordance(scheme, missingSitesFlag);
    }

    /** The type of the event (i.e. either SNP or INDEL) */
    public VariantContext.Type VARIANT_TYPE;

    /** The name of the 'truth' sample */
    public String TRUTH_SAMPLE;

    /** The name of the 'call' sample */
    public String CALL_SAMPLE;

    /** The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN)) */
    public double HET_SENSITIVITY;

    /** The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP)) */
    public double HET_PPV;

    /** The specificity for all heterozygous variants cannot be calculated */
    public double HET_SPECIFICITY;

    /** The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN)) */
    public double HOMVAR_SENSITIVITY;

    /** The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP)) */
    public double HOMVAR_PPV;

    /** The specificity for all homozygous variants cannot be calculated. */
    public double HOMVAR_SPECIFICITY;

    /** The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN)) */
    public double VAR_SENSITIVITY;

    /** The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP)) */
    public double VAR_PPV;

    /** The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN)) */
    public double VAR_SPECIFICITY;

    /** The genotype concordance for all possible states.
     *  Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made
     */
    public double GENOTYPE_CONCORDANCE;

    /** The non-ref genotype concordance, ie for all var states only.
     * Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made
     */
    public double NON_REF_GENOTYPE_CONCORDANCE;
}