Convenience method to check if a file is a vcf file.


>>> is_vcf(None)
>>> is_vcf("./foo")
>>> is_vcf("./foo.vcf")
>>> is_vcf("./foo.vcf.GZ")
True, vcf_file_name, ref_file_name)

Writes out a VCF-style file (which seems to be minimally handleable by vcftools and pyvcf) of the AA differences between sequences and the reference. This is a similar format created/used by read_in_vcf except that there is one of these dicts (with sequences, reference, positions) for EACH gene.

Also writes out a fasta of the reference alignment.

EBH 12 Dec 2017, output_filename, dropped_samps)