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