diff --git a/bseq.c b/bseq.c
index 2ee29b2..2cf9467 100644
--- a/bseq.c
+++ b/bseq.c
@@ -7,6 +7,25 @@
 #include "kseq.h"
 KSEQ_INIT2(, gzFile, gzread)
 
+unsigned char seq_comp_table[256] = {
+	  0,   1,	2,	 3,	  4,   5,	6,	 7,	  8,   9,  10,	11,	 12,  13,  14,	15,
+	 16,  17,  18,	19,	 20,  21,  22,	23,	 24,  25,  26,	27,	 28,  29,  30,	31,
+	 32,  33,  34,	35,	 36,  37,  38,	39,	 40,  41,  42,	43,	 44,  45,  46,	47,
+	 48,  49,  50,	51,	 52,  53,  54,	55,	 56,  57,  58,	59,	 60,  61,  62,	63,
+	 64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
+	'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z',	91,	 92,  93,  94,	95,
+	 64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
+	'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127,
+	128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
+	144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
+	160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,
+	176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,
+	192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
+	208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,
+	224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239,
+	240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255
+};
+
 #define CHECK_PAIR_THRES 1000000
 
 struct mm_bseq_file_s {
diff --git a/bseq.h b/bseq.h
index 9124273..5dfe095 100644
--- a/bseq.h
+++ b/bseq.h
@@ -24,6 +24,7 @@ mm_bseq1_t *mm_bseq_read_multi(int n_fp, mm_bseq_file_t **fp, int chunk_size, in
 int mm_bseq_eof(mm_bseq_file_t *fp);
 
 extern unsigned char seq_nt4_table[256];
+extern unsigned char seq_comp_table[256];
 
 static inline int mm_qname_same(const char *s1, const char *s2)
 {
@@ -31,11 +32,25 @@ static inline int mm_qname_same(const char *s1, const char *s2)
 	l1 = strlen(s1);
 	l2 = strlen(s2);
 	if (l1 != l2 || l1 < 3) return 0;
-	if (!(s1[l1-1] >= '1' && s1[l1-1] <= '2' && s1[l1-2] == '/')) return 0;
-	if (!(s2[l2-1] >= '1' && s2[l2-1] <= '2' && s2[l2-2] == '/')) return 0;
+	if (!(s1[l1-1] >= '0' && s1[l1-1] <= '9' && s1[l1-2] == '/')) return 0;
+	if (!(s2[l2-1] >= '0' && s2[l2-1] <= '9' && s2[l2-2] == '/')) return 0;
 	return (strncmp(s1, s2, l1 - 2) == 0);
 }
 
+static inline void mm_revcomp_bseq(mm_bseq1_t *s)
+{
+	int i, t, l = s->l_seq;
+	for (i = 0; i < l>>1; ++i) {
+		t = s->seq[l - i - 1];
+		s->seq[l - i - 1] = seq_comp_table[(uint8_t)s->seq[i]];
+		s->seq[i] = seq_comp_table[t];
+	}
+	if (l&1) s->seq[l>>1] = seq_comp_table[(uint8_t)s->seq[l>>1]];
+	if (s->qual)
+		for (i = 0; i < l>>1; ++i)
+			t = s->qual[l - i - 1], s->qual[l - i - 1] = s->qual[i], s->qual[i] = t;
+}
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/format.c b/format.c
index 949c0cd..deadbe1 100644
--- a/format.c
+++ b/format.c
@@ -213,17 +213,6 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
 		write_cs(km, s, mi, t, r);
 }
 
-static char comp_tab[] = {
-	  0,   1,	2,	 3,	  4,   5,	6,	 7,	  8,   9,  10,	11,	 12,  13,  14,	15,
-	 16,  17,  18,	19,	 20,  21,  22,	23,	 24,  25,  26,	27,	 28,  29,  30,	31,
-	 32,  33,  34,	35,	 36,  37,  38,	39,	 40,  41,  42,	43,	 44,  45,  46,	47,
-	 48,  49,  50,	51,	 52,  53,  54,	55,	 56,  57,  58,	59,	 60,  61,  62,	63,
-	 64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
-	'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z',	91,	 92,  93,  94,	95,
-	 64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
-	'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127
-};
-
 void mm_write_sam_SQ(const mm_idx_t *idx)
 {
 	uint32_t i;
@@ -233,12 +222,13 @@ void mm_write_sam_SQ(const mm_idx_t *idx)
 
 static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
 {
+	extern unsigned char seq_comp_table[256];
 	if (rev) {
 		int i;
 		str_enlarge(s, l);
 		for (i = 0; i < l; ++i) {
 			int c = seq[l - 1 - i];
-			s->s[s->l + i] = c < 128 && comp? comp_tab[c] : c;
+			s->s[s->l + i] = c < 128 && comp? seq_comp_table[c] : c;
 		}
 		s->l += l;
 	} else str_copy(s, seq, seq + l);
diff --git a/main.c b/main.c
index c1ec8bb..b782703 100644
--- a/main.c
+++ b/main.c
@@ -37,6 +37,9 @@ static struct option long_options[] = {
 	{ "cost-non-gt-ag", required_argument, 0, 0 },
 	{ "no-sam-sq",      no_argument,       0, 0 },
 	{ "sr",             no_argument,       0, 0 },
+	{ "multi-segment",  no_argument,       0, 0 },
+	{ "2nd-seg-rev",    no_argument,       0, 0 },
+	{ "2nd-seg-for",    no_argument,       0, 0 },
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -115,6 +118,9 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
 		else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq
 		else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
+		else if (c == 0 && long_idx ==14) opt.flag |= MM_F_MULTI_SEG; // --multi-seg
+		else if (c == 0 && long_idx ==15) opt.flag |= MM_F_SEG_REV; // --2nd-seg-rev
+		else if (c == 0 && long_idx ==16) opt.flag &= ~MM_F_SEG_REV; // --2nd-seg-for
 		else if (c == 'V') {
 			puts(MM_VERSION);
 			return 0;
diff --git a/map.c b/map.c
index 50dcb6d..e8f4c8a 100644
--- a/map.c
+++ b/map.c
@@ -75,7 +75,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		mo->min_dp_max = 200;
 	} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
 		io->is_hpc = 0, io->k = 21, io->w = 11;
-		mo->flag |= MM_F_SR | MM_F_MULTI_SEG;
+		mo->flag |= MM_F_SR | MM_F_MULTI_SEG | MM_F_SEG_REV;
 		mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
 		mo->max_gap = 100;
 		mo->pri_ratio = 0.5f;
@@ -161,7 +161,7 @@ static void collect_minimizers(const mm_mapopt_t *opt, const mm_idx_t *mi, int n
 	for (i = n = 0; i < n_segs; ++i) {
 		mm_sketch(b->km, seqs[i], qlens[i], mi->w, mi->k, i, mi->is_hpc, &b->mini);
 		for (j = n; j < b->mini.n; ++j)
-			b->mini.a[j].x += sum << 1;
+			b->mini.a[j].y += sum << 1;
 		if (opt->sdust_thres > 0) // mask low-complexity minimizers
 			b->mini.n = n + mm_dust_minier(b->mini.n - n, b->mini.a + n, qlens[i], seqs[i], opt->sdust_thres, b->sdb);
 		sum += qlens[i], n = b->mini.n;
@@ -295,6 +295,7 @@ void mm_map_multi(const mm_idx_t *mi, int n_segs, const int *qlens, const char *
 		seg = mm_seg_gen(b->km, n_segs, qlens, n_regs0, regs0, n_regs, regs, a);
 		free(regs0);
 		for (i = 0; i < n_segs; ++i) {
+			mm_set_parent(b->km, opt->mask_level, n_regs[i], regs[i], opt->a * 2 + opt->b);
 			regs[i] = align_regs(opt, mi, b->km, qlens[i], seqs[i], &n_regs[i], regs[i], seg[i].a);
 			mm_set_mapq(n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len);
 		}
@@ -344,10 +345,24 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
 	qlens = (int*)kmalloc(b->km, s->n_seg[i] * sizeof(int));
 	qseqs = (const char**)kmalloc(b->km, s->n_seg[i] * sizeof(const char**));
 	for (j = 0; j < s->n_seg[i]; ++j) {
+		if (j > 0 && (s->p->opt->flag & MM_F_SEG_REV))
+			mm_revcomp_bseq(&s->seq[off + j]);
 		qlens[j] = s->seq[off + j].l_seq;
 		qseqs[j] = s->seq[off + j].seq;
 	}
 	mm_map_multi(s->p->mi, s->n_seg[i], qlens, qseqs, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
+	if (s->n_seg[i] > 1 && (s->p->opt->flag & MM_F_SEG_REV))
+		for (j = 1; j < s->n_seg[i]; ++j) { // flip the query strand and coordinate to the original read strand
+			int k, t;
+			mm_revcomp_bseq(&s->seq[off + j]);
+			for (k = 0; k < s->n_reg[off + j]; ++k) {
+				mm_reg1_t *r = &s->reg[off + j][k];
+				t = r->qs;
+				r->qs = qlens[j] - r->qe;
+				r->qe = qlens[j] - t;
+				r->rev = !r->rev;
+			}
+		}
 	kfree(b->km, qlens);
 	kfree(b->km, qseqs);
 }
diff --git a/minimap.h b/minimap.h
index 46e66e7..742a4a7 100644
--- a/minimap.h
+++ b/minimap.h
@@ -18,6 +18,7 @@
 #define MM_F_NO_SAM_SQ   0x800
 #define MM_F_SR          0x1000
 #define MM_F_MULTI_SEG   0x2000
+#define MM_F_SEG_REV     0x4000
 
 #define MM_IDX_MAGIC   "MMI\2"