align2alleles.py will skip fixed variants when --min-allele-count is greater than 1

When align2alleles.py is called with --min-allele-count > 1 and a SNP is present in all samples, the reference allele will not be included here:

https://github.com/jts/ncov-tools/blob/master/workflow/scripts/align2alleles.py#L82

This is not unintuitive so should be changed so the reference allele is always included