Add support for VCF output.

[jonathancrabtree]

Add option to produce VCF output. Most likely the reference for this will be the genome reference / hg38, not the reference MEI consensus sequence, so we're essentially subsetting the input VCF and decorating it with a few computed values. Might also look into producing a multi-sample VCF that could be used to do cross-sample comparisons.

[jonathancrabtree]

Look into bcftools merge for creating the multi-sample files.

[jonathancrabtree]

Output checked with vcf-validator:

% vcf-validator -d hg38-HG00171-h1-PAV-MEs-v1.4.2-40-80-95bp-90-90-SVA-40-90-unique-seq.vcf