Implement VCF output file

[kjohnsen]

As of yet, the old .writeCandidateVCFs function (see in history) didn't work because it only takes VCF objects (which can be created from VRanges objects), but we work with a GRanges object from the VEP step on. Thus, we can't write a VCF output file using that function.

Two ideas to make output VCFs possible:

1. Parse row names from GRanges to get the ref column needed to convert GRanges to VRanges
2. Output a VCF object from ensemblVEP. This would require refactoring the functions that follow (filtering, scoring, and ranking) to work with a VCF object rather than GRanges.