Fixed bug with vcfallelicprimitives handling of monomorphic reference mnps which are produced by some snp callers

e.g.

X       40      .       GGG    .    100  PASS      LEN=1,2;TYPE=snp,complex GT      0|0     0|0     .

was being translated to this. Note the invalid alternate allele field.

X       40      .       GGG    .GG,.    100  PASS      LEN=1,2;TYPE=snp,complex GT      0|0     0|0     .