diff --git a/format.c b/format.c
index 6d8fa88..b292857 100644
--- a/format.c
+++ b/format.c
@@ -76,7 +76,7 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
 	write_tags(s, r);
 	if (r->p) {
 		uint32_t k;
-		mm_sprintf_lite(s, "cg:Z:");
+		mm_sprintf_lite(s, "\tcg:Z:");
 		for (k = 0; k < r->p->n_cigar; ++k)
 			mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
 	}
@@ -112,7 +112,7 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
 	s->l = 0;
 	if (r->rev) flag |= 0x10;
 	if (r->parent != r->id) flag |= 0x100;
-	if (r->id != 0) flag |= 0x800; // TODO: make sure this is always working!
+	else if (!r->sam_pri) flag |= 0x800;
 	mm_sprintf_lite(s, "%s\t%d\t%s\t%d\t%d\t", t->name, flag, mi->seq[r->rid].name, r->rs+1, r->mapq);
 	if (r->p) { // TODO: using hard clippings
 		uint32_t k, clip_len = r->rev? t->l_seq - r->qe : r->qs;
diff --git a/hit.c b/hit.c
index ff42d2c..cfae504 100644
--- a/hit.c
+++ b/hit.c
@@ -27,6 +27,7 @@ void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
 	if (n <= 0 || n >= r->cnt) return;
 	*r2 = *r;
 	r2->id = -1;
+	r2->sam_pri = 0;
 	r2->p = 0;
 	r2->cnt = r->cnt - n;
 	r2->score = (int32_t)(r->score * ((float)r2->cnt / r->cnt) + .499);
@@ -65,7 +66,7 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r) // and compu
 
 void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,parent} in sync; also reset id
 {
-	int *tmp, i, max_id = -1, n_tmp;
+	int *tmp, i, max_id = -1, n_tmp, n_pri;
 	if (n_regs <= 0) return;
 	for (i = 0; i < n_regs; ++i)
 		max_id = max_id > regs[i].id? max_id : regs[i].id;
@@ -74,7 +75,7 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
 	for (i = 0; i < n_tmp; ++i) tmp[i] = -1;
 	for (i = 0; i < n_regs; ++i)
 		if (regs[i].id >= 0) tmp[regs[i].id] = i;
-	for (i = 0; i < n_regs; ++i) {
+	for (i = n_pri = 0; i < n_regs; ++i) {
 		mm_reg1_t *r = &regs[i];
 		r->id = i;
 		if (r->parent == MM_PARENT_TMP_PRI)
@@ -82,6 +83,9 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
 		else if (r->parent >= 0 && tmp[r->parent] >= 0)
 			r->parent = tmp[r->parent];
 		else r->parent = MM_PARENT_UNSET;
+		if (r->id == r->parent) {
+			if (n_pri++ == 0) r->sam_pri = 1;
+		}
 	}
 	kfree(km, tmp);
 }
diff --git a/main.c b/main.c
index 3b7542a..47712d3 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r114-pre"
+#define MM_VERSION "2.0-r115-pre"
 
 void liftrlimit()
 {
diff --git a/minimap.h b/minimap.h
index 04c3391..f8635c3 100644
--- a/minimap.h
+++ b/minimap.h
@@ -60,7 +60,7 @@ typedef struct {
 	int32_t qs, qe, rs, re;
 	int32_t parent, subsc;
 	int32_t as;
-	uint32_t mapq:8, split:2, n_sub:22; // TODO: n_sub is not used for now
+	uint32_t mapq:8, split:2, sam_pri:1, n_sub:21; // TODO: n_sub is not used for now
 	mm_extra_t *p;
 } mm_reg1_t;