Variant

[pnrobinson]

@lnrekerle

This is dangerous because perhaps the user gives us some other input.

 if reference == 'hg37':
                    ens = pyensembl.ensembl_grch37
                else:
                    ens = pyensembl.ensembl_grch38
                myVar = vc.Variant(contig, start, ref, alt, ensembl = ens)

it should probably be

 if reference == 'hg37':
                    ens = pyensembl.ensembl_grch37
                elif reference == 'hg38':
                    ens = pyensembl.ensembl_grch38
              else:
                    raise ValueException("some message")
    myVar = vc.Variant(contig, start, ref, alt, ensembl = ens)

[lnrekerle]

Done in Develop