making alternate allele frequency work in the case of non-diploid genotypes

I edited ```vcf.model.aaf``` to not break and give the correct answer in the case of haploid (or diploid, triploid, etc.) genotypes. I also added test cases for this in a new vcf example file called example-4.1-ploidy.vcf.

Note this is also an issue in ```vcf.model.nucl_diversity```, which calculates ```num_chroms``` as 2 * the number of called genotypes. Thoughts on changing this?