Allow reference sequence as input to fill in uncalled variants for a fasta alignment

[kche309]

Fill in uncalled sites in the VCF with the REF allele in the reference fasta.
The reference fasta file is assumed to be sorted with 1-based positions 1, ..., N.

Usage:

cd vcf2fasta
python src/vcf2fasta.py <vcf file> <output fasta> --ref <ref fasta>

Example:

python src/vcf2fasta.py data/variants.vcf data/test.fasta --ref data/filtered_sequence.fna     

Future TODO:
A more robust format to be implemented in the future could:

• use a BED style file with chrom, pos, REF as the header, or
• use a Reference VCF with chrom, pos, REF as the fields