Prevent empty PL fields on BCF output with "call -C alleles"

overerd · Nov 18, 2015 · 8e8679d · 8e8679d
1 parent 37b0ddc
commit 8e8679d
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/mcall.c b/mcall.c
@@ -1332,6 +1332,7 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
                 if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(unseen,unseen);
                 new_pl[k] = ori_pl[k_ori];
             }
+            if ( !k && new_pl[k]==bcf_int32_vector_end ) new_pl[k]=bcf_int32_missing;
         }
         ori_pl += npls_ori;
         new_pl += npls_new;