Primer3 should accept a variant lookup Path

[msto]

Much like Primer3 accepts a Path to the input FASTA, it would be more ergonomic if the class accepted a Path to a VCF instead of requiring the user to construct a VariantLookup.

[emmcauley]

We have two VariantLookup objects and corresponding constructors: one is recommended for smaller VCFs and one is recommended for bigger VCFs. I'm envisioning that we could take a path to a VCF, determine the appropriate constructor, and construct the VariantLookup object under the hood.

@msto:
-do you agree with my thoughts above? Did I miss anything?
-if so, what do you think is the best way for us to check the given VCF path to see which constructor would be the appropriate one to call?

[emmcauley]

plan:

• add to the Primer3 constructor, a list of VCFs, and a boolean flag (should we load into memory or query every time we need something?) -- the bool will trigger what variant lookup to build; but the default will be the disk-based one

[msto]

Yes, that's exactly what I had in mind 🙂