n_alt_count and n_ref_count corrupted at recurrent sites in maf2maf reannotation

[sggaffney]

I've noticed in my last two runs of maf2maf that n_alt_count and n_ref_count can be altered during reannotation by maf2maf.pl. This occurs when a variant is present in multiple samples. For these recurrent variants, the values of n_alt_count and n_ref_count can be erroneously copied from one sample to another. Apologies for not having generated a minimal reproducible example at this time, but I wanted to share asap.