void
make_record_haploid(VcfRecord& vcfr) const {
const char* gt(vcfr.GetSampleVal("GT"));
if(NULL == gt) return;
parse_gt(gt,_gti);
if(_gti.size() == 2) { // record is diploid
if(_gti[0] == _gti[1]) {
// change GT:
static const char* unknown(".");
const char* val(unknown);
if(_gti[0]>=0) {
val=_intstr.get32(_gti[0]);
}
vcfr.SetSampleVal("GT",val);
// move PL field to 'backup' OPL field:
const char* pl(vcfr.GetSampleVal("PL"));
if(NULL != pl) {
vcfr.SetSampleVal(_shopt.orig_pl_tag.c_str(),pl);
vcfr.DeleteSampleKeyVal("PL");
}
} else {
vcfr.AppendFilter(_shopt.haploid_conflict_label.c_str());
}
}
}
