int i;
for (i = 0; i < 9; ++i) em[i] = -1.;
}
- if ( !(vc.flag&VC_KEEPALT) && vc.flag&VC_CALL && vc.min_ma_lrt>=0 )
+ if ( !(vc.flag&VC_KEEPALT) && (vc.flag&VC_CALL) && vc.min_ma_lrt>=0 )
{
bcf_p1_set_ploidy(b, p1); // could be improved: do this per site to allow pseudo-autosomal regions
- int gts = call_multiallelic_gt(b,p1,vc.min_ma_lrt);
+ int gts = call_multiallelic_gt(b, p1, vc.min_ma_lrt, vc.flag&VC_VARONLY);
if ( gts<=1 && vc.flag & VC_VARONLY ) continue;
}
else if (vc.flag & VC_CALL) { // call variants