Warning on incompatible multiallelic VCF

[VelNZ]

Good job putting this together! It's very useful for moving away from the limitations of GEMINI with regard to static files and blobs.

I tried to feed a VCF with multiallelic sites into vcf2db (MySQL mode) and it gave a "Operand should contain 1 column(s)" error. After looking at the line it was complaining about, I found it was a multiallelic site and the error arose because the AF had two values.

It would be useful to detect that the VCF has multiallelic sites and state vcf2db does not support them and direct to vt for decomposition/normalization and exit gracefully.

[brentp]

thanks for reporting. I punted on this for now because I wanted to decide how to handle it. sqlite is very permissive about what goes in, so it wont give that error (though sqlalchemy likely will). I may use ",".join(alt_list) to allow this and give a warning.
this is vaguely related to #1.