Return N for ref allele in pos uncovered by ref
Return N for ref allele in pos uncovered by ref

This arose during processing of a CGI var file originating from LFR
data (not sure, but LFR is an advanced technique, so it's possible CGI
is calling some positions that aren't called in reference).

PersonalGenomesOrg/archive-genevieve-201505,PersonalGenomesOrg/archive-genevieve-201505,PersonalGenomesOrg/archive-genevieve-201505