diff --git a/format.c b/format.c
index b292857..c81aac1 100644
--- a/format.c
+++ b/format.c
@@ -125,7 +125,7 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
 	} else mm_sprintf_lite(s, "*");
 	mm_sprintf_lite(s, "\t*\t0\t0\t");
 	if ((flag & 0x900) == 0) sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
-	else if (flag & 0x100) mm_sprintf_lite(s, "\t*");
+	else if (flag & 0x100) mm_sprintf_lite(s, "*");
 	else sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev);
 	mm_sprintf_lite(s, "\t*"); // quality
 	write_tags(s, r);
diff --git a/hit.c b/hit.c
index cfae504..4c84191 100644
--- a/hit.c
+++ b/hit.c
@@ -3,22 +3,37 @@
 #include "mmpriv.h"
 #include "kalloc.h"
 
-mm_reg1_t *mm_gen_regs(int qlen, int n_u, uint64_t *u, mm128_t *a) // convert chains to hits
+mm_reg1_t *mm_gen_regs(void *km, int qlen, int n_u, uint64_t *u, mm128_t *a) // convert chains to hits
 {
+	mm128_t *z, tmp;
 	mm_reg1_t *r;
 	int i, k;
-	r = (mm_reg1_t*)calloc(n_u, sizeof(mm_reg1_t));
+
+	if (n_u == 0) return 0;
+
+	// sort by score
+	z = (mm128_t*)kmalloc(km, n_u * 16);
 	for (i = k = 0; i < n_u; ++i) {
+		z[i].x = u[i] >> 32;
+		z[i].y = (uint64_t)k << 32 | (int32_t)u[i];
+		k += (int32_t)u[i];
+	}
+	radix_sort_128x(z, z + n_u);
+	for (i = 0; i < n_u>>1; ++i) // reverse, s.t. larger score first
+		tmp = z[i], z[i] = z[n_u-1-i], z[n_u-1-i] = tmp;
+
+	// populate r[]
+	r = (mm_reg1_t*)calloc(n_u, sizeof(mm_reg1_t));
+	for (i = 0; i < n_u; ++i) {
 		mm_reg1_t *ri = &r[i];
 		ri->id = i;
 		ri->parent = MM_PARENT_UNSET;
-		ri->subsc = 0;
-		ri->score = u[i]>>32;
-		ri->cnt = (int32_t)u[i];
-		ri->as = k;
+		ri->score = z[i].x;
+		ri->cnt = (int32_t)z[i].y;
+		ri->as = z[i].y >> 32;
 		mm_reg_set_coor(ri, qlen, a);
-		k += ri->cnt;
 	}
+	kfree(km, z);
 	return r;
 }
 
diff --git a/main.c b/main.c
index 5f95cc9..c0d03a5 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r117-pre"
+#define MM_VERSION "2.0-r118-pre"
 
 void liftrlimit()
 {
diff --git a/map.c b/map.c
index df98af4..f6c0ef9 100644
--- a/map.c
+++ b/map.c
@@ -235,7 +235,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
 	kfree(b->km, m);
 
 	n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, n_a, a, &u, b->km);
-	regs = mm_gen_regs(qlen, n_u, u, a);
+	regs = mm_gen_regs(b->km, qlen, n_u, u, a);
 	*n_regs = n_u;
 	if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
 		mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, n_regs, regs);
diff --git a/mmpriv.h b/mmpriv.h
index ee19d0f..65f82a1 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -36,7 +36,7 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
 int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int64_t n, mm128_t *a, uint64_t **_u, void *km);
 mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);
 
-mm_reg1_t *mm_gen_regs(int qlen, int n_u, uint64_t *u, mm128_t *a);
+mm_reg1_t *mm_gen_regs(void *km, int qlen, int n_u, uint64_t *u, mm128_t *a);
 void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a);
 void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs);
 void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1_t *r);