Add VCF output support

[niemasd]

For pure samples, consensus sequence is probably most helpful (along with base/insertion counts for confidence), but for a mixed sample (e.g. wastewater), even though the base/insertion counts are probably good enough, it might still be good to output a VCF file (e.g. to make it easy to see base/insertion frequencies just at high-coverage sites that differ from the reference genome). This should be pretty easy to do: basically do the same thing as outputting the base/insertion counts, but just (1) check that the total count is above the minimum coverage, (2) compute proportions from the counts, and (3) write it in the VCF format specifically