7b17bcd0af2c4609a5dd3e83b007d3f383cf7ae9,java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java,MendelianViolationEvaluator,isViolation,#VariantContext#Genotype#Genotype#Genotype#,141

Before Change


        //VariantContext momVC = vc.subContextFromGenotypes(momG);
        //VariantContext dadVC = vc.subContextFromGenotypes(dadG);
        int i = 0;
        for ( Allele momAllele : momG.getAlleles() ) {
            for ( Allele dadAllele : dadG.getAlleles() ) {
                if ( momAllele.isCalled() && dadAllele.isCalled() ) {
                    Genotype possibleChild = new Genotype("possibleGenotype" + i, Arrays.asList(momAllele, dadAllele));
                    if ( childG.sameGenotype(possibleChild, false) ) {
                        return false;
                    }
                }

After Change


    }

    public static boolean isViolation(VariantContext vc, Genotype momG, Genotype dadG, Genotype childG ) {
        return isViolation(vc, momG.getAlleles(), dadG.getAlleles(), childG.getAlleles());
    }

    public static boolean isViolation(VariantContext vc, List<Allele> momA, List<Allele> dadA, List<Allele> childA ) {