diff --git a/chain.c b/chain.c
index 8894d44..37c920a 100644
--- a/chain.c
+++ b/chain.c
@@ -56,7 +56,8 @@ int mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cn
 				int c_log, c_lin;
 				c_lin = (int)(dd * .01 * avg_qspan);
 				c_log = ilog2_32(dd);
-				sc -= c_lin < c_log? c_lin : c_log;
+				if (dr > dq) sc -= c_lin < c_log? c_lin : c_log;
+				else sc -= c_lin + (c_log>>1);
 			} else sc -= (int)(dd * .01 * avg_qspan) + (ilog2_32(dd)>>1);
 			sc += f[j];
 			if (sc > max_f) {
diff --git a/format.c b/format.c
index fd51c00..02cf3be 100644
--- a/format.c
+++ b/format.c
@@ -122,7 +122,7 @@ static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
 	if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
 }
 
-void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag)
+void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag, int intron_thres)
 {
 	s->l = 0;
 	mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
@@ -136,8 +136,12 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
 	if (r->p && (opt_flag & MM_F_OUT_CG)) {
 		uint32_t k;
 		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]);
+		for (k = 0; k < r->p->n_cigar; ++k) {
+			int op = r->p->cigar[k]&0xf, len = r->p->cigar[k]>>4;
+			if (intron_thres > 0 && op == 2 && len >= intron_thres)
+				mm_sprintf_lite(s, "%dN", len);
+			else mm_sprintf_lite(s, "%d%c", len, "MID"[op]);
+		}
 	}
 	if (r->p && (opt_flag & MM_F_OUT_CS))
 		write_cs(km, s, mi, t, r);
@@ -167,7 +171,7 @@ static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
 	} else str_copy(s, seq, seq + l);
 }
 
-void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs)
+void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs, int intron_thres)
 {
 	int flag = 0;
 	s->l = 0;
@@ -186,8 +190,12 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
 			uint32_t k, clip_len = r->rev? t->l_seq - r->qe : r->qs;
 			int clip_char = (flag&0x800)? 'H' : 'S';
 			if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
-			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]);
+			for (k = 0; k < r->p->n_cigar; ++k) {
+				int op = r->p->cigar[k]&0xf, len = r->p->cigar[k]>>4;
+				if (intron_thres > 0 && op == 2 && len >= intron_thres)
+					mm_sprintf_lite(s, "%dN", len);
+				else mm_sprintf_lite(s, "%d%c", len, "MID"[op]);
+			}
 			clip_len = r->rev? r->qs : t->l_seq - r->qe;
 			if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
 		} else mm_sprintf_lite(s, "*");
diff --git a/main.c b/main.c
index 5ac5262..32a2bc7 100644
--- a/main.c
+++ b/main.c
@@ -8,7 +8,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r279-dirty"
+#define MM_VERSION "2.0-r280-dirty"
 
 void liftrlimit()
 {
diff --git a/map.c b/map.c
index 6e7b869..dd1624c 100644
--- a/map.c
+++ b/map.c
@@ -344,19 +344,24 @@ static void *worker_pipeline(void *shared, int step, void *in)
 		void *km = 0;
         step_t *s = (step_t*)in;
 		const mm_idx_t *mi = p->mi;
+		int intron_thres = -1;
 		for (i = 0; i < p->n_threads; ++i) mm_tbuf_destroy(s->buf[i]);
 		free(s->buf);
+		if (p->opt->flag & MM_F_CDNA)
+			intron_thres = (int)((float)(p->opt->q2 - p->opt->q) / p->opt->e + 0.999f);
 		if ((p->opt->flag & MM_F_OUT_CS) && !(mm_dbg_flag & MM_DBG_NO_KALLOC)) km = km_init();
 		for (i = 0; i < s->n_seq; ++i) {
 			mm_bseq1_t *t = &s->seq[i];
 			for (j = 0; j < s->n_reg[i]; ++j) {
 				mm_reg1_t *r = &s->reg[i][j];
-				if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, r, s->n_reg[i], s->reg[i]);
-				else mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
+				if (p->opt->flag & MM_F_OUT_SAM)
+					mm_write_sam(&p->str, mi, t, r, s->n_reg[i], s->reg[i], intron_thres);
+				else
+					mm_write_paf(&p->str, mi, t, r, km, p->opt->flag, intron_thres);
 				puts(p->str.s);
 			}
 			if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
-				mm_write_sam(&p->str, 0, t, 0, 0, 0);
+				mm_write_sam(&p->str, 0, t, 0, 0, 0, 0);
 				puts(p->str.s);
 			}
 			for (j = 0; j < s->n_reg[i]; ++j) free(s->reg[i][j].p);
diff --git a/mmpriv.h b/mmpriv.h
index 1c03ae7..6f22b0b 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -40,8 +40,8 @@ void radix_sort_128x(mm128_t *beg, mm128_t *end);
 void radix_sort_64(uint64_t *beg, uint64_t *end);
 uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
 
-void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag);
-void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);
+void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag, int intron_thres);
+void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs, int intron_thres);
 int mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, 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);