diff --git a/align.c b/align.c
index 4abed92..9bb61bd 100644
--- a/align.c
+++ b/align.c
@@ -65,7 +65,7 @@ static int mm_check_zdrop(const uint8_t *qseq, const uint8_t *tseq, uint32_t n_c
 static void mm_update_extra(mm_extra_t *p, const uint8_t *qseq, const uint8_t *tseq, const int8_t *mat, int8_t q, int8_t e)
 {
 	uint32_t k, l, toff = 0, qoff = 0;
-	int32_t s = 0, max = 0, n_gtag = 0, n_ctac = 0;
+	int32_t s = 0, max = 0;
 	if (p == 0) return;
 	for (k = 0; k < p->n_cigar; ++k) {
 		uint32_t op = p->cigar[k]&0xf, len = p->cigar[k]>>4;
@@ -99,14 +99,10 @@ static void mm_update_extra(mm_extra_t *p, const uint8_t *qseq, const uint8_t *t
 			uint8_t b[4];
 			b[0] = tseq[toff], b[1] = tseq[toff+1];
 			b[2] = tseq[toff+len-2], b[3] = tseq[toff+len-1];
-			if (memcmp(b, "\2\3\0\2", 4) == 0) ++n_gtag;
-			else if (memcmp(b, "\1\3\0\1", 4) == 0) ++n_ctac;
 			toff += len, p->blen += len;
 		}
 	}
 	p->dp_max = max;
-	if (n_gtag > n_ctac) p->trans_strand = 1;
-	else if (n_gtag < n_ctac) p->trans_strand = 2;
 }
 
 static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) // TODO: this calls the libc realloc()
@@ -284,7 +280,6 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	if (opt->flag & MM_F_SPLICE) {
 		if (splice_flag & MM_F_SPLICE_FOR) extra_flag |= rev? KSW_EZ_SPLICE_REV : KSW_EZ_SPLICE_FOR;
 		if (splice_flag & MM_F_SPLICE_REV) extra_flag |= rev? KSW_EZ_SPLICE_FOR : KSW_EZ_SPLICE_REV;
-		if (splice_flag & MM_F_SPLICE_BOTH) extra_flag |= KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV;
 	}
 
 	// compute rs0 and qs0
@@ -468,7 +463,7 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
 	memset(&ez, 0, sizeof(ksw_extz_t));
 	for (i = 0; i < n_regs; ++i) {
 		mm_reg1_t r2;
-		if ((opt->flag&MM_F_SPLICE) && (opt->flag&MM_F_SPLICE_FOR) && (opt->flag&MM_F_SPLICE_REV)) {
+		if ((opt->flag&MM_F_SPLICE) && (opt->flag&MM_F_SPLICE_FOR) && (opt->flag&MM_F_SPLICE_REV)) { // then do two rounds of alignments for both strands
 			mm_reg1_t s[2], s2[2];
 			int which, trans_strand;
 			s[0] = s[1] = regs[i];
@@ -485,9 +480,9 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
 				free(s[0].p);
 			}
 			regs[i].p->trans_strand = trans_strand;
-		} else {
+		} else { // one round of alignment
 			mm_align1(km, opt, mi, qlen, qseq0, &regs[i], &r2, a, &ez, opt->flag);
-			if ((opt->flag&MM_F_SPLICE) && !(opt->flag&MM_F_SPLICE_BOTH))
+			if (opt->flag&MM_F_SPLICE)
 				regs[i].p->trans_strand = opt->flag&MM_F_SPLICE_FOR? 1 : 2;
 		}
 		if (r2.cnt > 0) regs = mm_insert_reg(&r2, i, &n_regs, regs);
diff --git a/main.c b/main.c
index 4437625..2909ddc 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.2-r414-dirty"
+#define MM_VERSION "2.2-r421-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -124,11 +124,10 @@ int main(int argc, char *argv[])
 			if (x < 1.0) opt.mid_occ_frac = x, opt.mid_occ = 0;
 			else opt.mid_occ = (int)(x + .499);
 		} else if (c == 'u') {
-			if (*optarg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV;
-			else if (*optarg == 'B') opt.flag |= MM_F_SPLICE_BOTH;
-			else if (*optarg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV;
-			else if (*optarg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR;
-			else if (*optarg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV);
+			if (*optarg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV; // both strands
+			else if (*optarg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV; // match GT-AG
+			else if (*optarg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR; // match CT-AC (reverse complement of GT-AG)
+			else if (*optarg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV); // don't try to match the GT-AG signal
 			else {
 				fprintf(stderr, "[E::%s] unrecognized cDNA direction\n", __func__);
 				return 1;
diff --git a/map.c b/map.c
index 09a7024..924e2dd 100644
--- a/map.c
+++ b/map.c
@@ -38,8 +38,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 
 void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
 {
-	if (opt->flag & MM_F_SPLICE_BOTH)
-		opt->flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV);
+	if ((opt->flag & MM_F_SPLICE_FOR) && (opt->flag & MM_F_SPLICE_REV))
+		opt->flag |= MM_F_SPLICE;
 	if (opt->mid_occ <= 0)
 		opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac);
 	if (mm_verbose >= 3)
diff --git a/minimap.h b/minimap.h
index ebe6715..74bf2ae 100644
--- a/minimap.h
+++ b/minimap.h
@@ -12,10 +12,9 @@
 #define MM_F_NO_QUAL     0x010
 #define MM_F_OUT_CG      0x020
 #define MM_F_OUT_CS      0x040
-#define MM_F_SPLICE      0x080
-#define MM_F_SPLICE_FOR  0x100
-#define MM_F_SPLICE_REV  0x200
-#define MM_F_SPLICE_BOTH 0x400
+#define MM_F_SPLICE      0x080 // splice mode
+#define MM_F_SPLICE_FOR  0x100 // match GT-AG
+#define MM_F_SPLICE_REV  0x200 // match CT-AC, the reverse complement of GT-AG
 #define MM_F_NO_SAM_SQ   0x800
 #define MM_F_SR          0x1000