Sites with different ALT alleles are dropped silently

If the same site in two vcf files have different ALT alleles, vtools-evaluate will silently ignore this position, even if the variants could be resolved. This is because it used cyvcf2 genotype codes where 0=homref, 1=heterozygous, 2=hom alt, 3=no call. These genotype codes only make sense when the ALT and REF alleles are identical.