private static void addReferenceGenotype(Variant variant, VariantStats stats, int alleleNumber) {
        int gtSum = 0;
        for (Integer gtCounts : stats.getGenotypeCount().values()) {
            gtSum += gtCounts;
        }
        Genotype genotype = new Genotype("0/0", variant.getReference(), variant.getAlternate());
        stats.addGenotype(genotype, alleleNumber / 2 - gtSum);  // assuming diploid sample! be careful if you copy this code!
    }
private static void addReferenceGenotype ( Variant variant , VariantStats stats , int alleleNumber ) { int gtSum = 0 ; for ( Integer gtCounts : stats . getGenotypeCount ( ) . values ( ) ) { gtSum += gtCounts ; } Genotype genotype = new Genotype ( "0/0" , variant . getReference ( ) , variant . getAlternate ( ) ) ; stats . addGenotype ( genotype , alleleNumber / 2 - gtSum ) ; }
Infers the 0/0 genotype count, given that: sum(Heterozygous) + sum(Homozygous) + sum(Reference) = alleleNumber/2
@param variant to retrieve the alleles to construct the genotype
@param stats where to add the 0/0 genotype count
@param alleleNumber total sum of alleles.