Reconsider default value for --use_allele_num

[bashir2]

When parsing annotation fields, it is probably safe to assume that ALLELE_NUM tag refers to one of the ALTs even without the user telling us explicitly. So the proposal is to set --use_allele_num to True by default and add logic to fall back to the alt string matching logic if ALLELE_NUM is absent or its values is out of bound.