diff --git a/align.c b/align.c
index d6b7dc5..a0d58af 100644
--- a/align.c
+++ b/align.c
@@ -242,7 +242,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 				if (r->cnt - (j + 1) >= opt->min_cnt) {
 					mm_split_reg(r, r2, j + 1, qlen, a);
 					if (j + 1 < opt->min_cnt)
-						r2->id = r->id, r->id = -1;
+						r2->id = r->id, r2->parent = r2->id, r->id = -1, r->parent = MM_PARENT_TMP_PRI;
 				}
 				break;
 			} else r->p->dp_score += ez->score;
@@ -305,6 +305,7 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
 		}
 	}
 	*n_regs_ = n_regs;
+	mm_sync_regs(km, n_regs, regs);
 	kfree(km, qseq0[0]); kfree(km, qseq0[1]);
 	kfree(km, ez.cigar);
 	mm_filter_regs(km, opt, n_regs_, regs);
diff --git a/hit.c b/hit.c
index 1222fba..fd0adfd 100644
--- a/hit.c
+++ b/hit.c
@@ -85,7 +85,7 @@ void mm_update_parent(void *km, float mask_level, int n, mm_reg1_t *r) // due to
 	if (n <= 0) return;
 	for (i = 0; i < n; ++i)
 		if (r[i].id == r[i].parent || r[i].parent < 0) ++n_pri;
-	if (n_pri <= 1) return;
+	if (n_pri <= 1) return; // FIXME: this is not right
 	w = (int*)kmalloc(km, n_pri * sizeof(int));
 	for (i = j = 0; i < n; ++i) // find the first primary
 		if (r[i].id == r[i].parent) break;