diff --git a/bwamem.c b/bwamem.c
index 346715c..27e341b 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -358,7 +358,7 @@ KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt)
 #define alnreg_hlt(a, b) ((a).score > (b).score || ((a).score == (b).score && (a).hash < (b).hash))
 KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt)
 
-int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun)
+int mem_sort_and_dedup2(int n, mem_alnreg_t *a, float mask_level_redun, int merge_bw)
 {
 	int m, i, j;
 	if (n <= 1) return n;
@@ -366,19 +366,39 @@ int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun)
 	for (i = 1; i < n; ++i) {
 		mem_alnreg_t *p = &a[i];
 		if (p->rb >= a[i-1].re) continue;
-		for (j = i - 1; j >= 0 && p->rb < a[j].re; --j) {
+		for (j = i - 1; j >= 0 && p->rid == a[j].rid && p->rb < a[j].re; --j) {
 			mem_alnreg_t *q = &a[j];
 			int64_t or, oq, mr, mq;
+			int is_merged = 0;
 			if (q->qe == q->qb) continue; // a[j] has been excluded
-			or = q->re - p->rb; // overlap length on the reference
-			oq = q->qb < p->qb? q->qe - p->qb : p->qe - q->qb; // overlap length on the query
-			mr = q->re - q->rb < p->re - p->rb? q->re - q->rb : p->re - p->rb; // min ref len in alignment
-			mq = q->qe - q->qb < p->qe - p->qb? q->qe - q->qb : p->qe - p->qb; // min qry len in alignment
-			if (or > mask_level_redun * mr && oq > mask_level_redun * mq) { // one of the hits is redundant
-				if (p->score < q->score) {
-					p->qe = p->qb;
-					break;
-				} else q->qe = q->qb;
+			if (merge_bw > 0 && q->qb < p->qb && q->qe < p->qe && q->re < p->re) {
+				int flag = 0;
+				int64_t l1, l2;
+				l1 = p->qb - q->qb, l2 = p->rb - q->rb;
+				if (l1 - l2 < merge_bw && l2 - l1 < merge_bw) ++flag;
+				l1 = p->qe - q->qe, l2 = p->re - q->re;
+				if (l1 - l2 < merge_bw && l2 - l1 < merge_bw) ++flag;
+				if (flag == 2) { // merge q into p
+					mem_alnreg_t t = *p;
+					*p = *q;
+					p->qe = t.qe, p->re = t.re;
+					p->score = p->score > t.score? p->score : t.score;
+					p->w = p->w > t.w? p->w : t.w;
+					q->qb = q->qe;
+					is_merged = 1;
+				}
+			}
+			if (is_merged == 0) {
+				or = q->re - p->rb; // overlap length on the reference
+				oq = q->qb < p->qb? q->qe - p->qb : p->qe - q->qb; // overlap length on the query
+				mr = q->re - q->rb < p->re - p->rb? q->re - q->rb : p->re - p->rb; // min ref len in alignment
+				mq = q->qe - q->qb < p->qe - p->qb? q->qe - q->qb : p->qe - p->qb; // min qry len in alignment
+				if (or > mask_level_redun * mr && oq > mask_level_redun * mq) { // one of the hits is redundant
+					if (p->score < q->score) {
+						p->qe = p->qb;
+						break;
+					} else q->qe = q->qb;
+				}
 			}
 		}
 	}
@@ -401,6 +421,11 @@ int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun)
 	return m;
 }
 
+int mem_sort_and_dedup(int n, mem_alnreg_t *a, float mask_level_redun)
+{
+	return mem_sort_and_dedup2(n, a, mask_level_redun, -1);
+}
+
 int mem_test_and_remove_exact(const mem_opt_t *opt, int n, mem_alnreg_t *a, int qlen)
 {
 	if (!(opt->flag & MEM_F_SELF_OVLP) || n == 0 || a->truesc != qlen * opt->a) return n;
@@ -960,7 +985,8 @@ mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntse
 		free(chn.a[i].seeds);
 	}
 	free(chn.a);
-	regs.n = mem_sort_and_dedup(regs.n, regs.a, opt->mask_level_redun);
+	if (opt->flag & MEM_F_MERGE_REG) regs.n = mem_sort_and_dedup2(regs.n, regs.a, opt->mask_level, opt->w);
+	else regs.n = mem_sort_and_dedup(regs.n, regs.a, opt->mask_level_redun);
 	if (opt->flag & MEM_F_SELF_OVLP)
 		regs.n = mem_test_and_remove_exact(opt, regs.n, regs.a, l_seq);
 	if (bwa_verbose >= 4) {
diff --git a/bwamem.h b/bwamem.h
index 53472fe..488d1cf 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -18,6 +18,7 @@ typedef struct __smem_i smem_i;
 #define MEM_F_NO_RESCUE 0x20
 #define MEM_F_SELF_OVLP 0x40
 #define MEM_F_ALN_REG   0x80
+#define MEM_F_MERGE_REG 0x100
 
 typedef struct {
 	int a, b;               // match score and mismatch penalty
diff --git a/fastmap.c b/fastmap.c
index 81c0f20..b898adb 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -53,7 +53,7 @@ int main_mem(int argc, char *argv[])
 
 	opt = mem_opt_init();
 	memset(&opt0, 0, sizeof(mem_opt_t));
-	while ((c = getopt(argc, argv, "epaFMCSPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:")) >= 0) {
+	while ((c = getopt(argc, argv, "epaFMCSPHVk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
 		else if (c == 'x') mode = optarg;
 		else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
@@ -69,6 +69,7 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE;
 		else if (c == 'e') opt->flag |= MEM_F_SELF_OVLP;
 		else if (c == 'F') opt->flag |= MEM_F_ALN_REG;
+		else if (c == 'V') opt->flag |= MEM_F_MERGE_REG;
 		else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
 		else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
 		else if (c == 'v') bwa_verbose = atoi(optarg);
@@ -147,7 +148,7 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -U INT        penalty for an unpaired read pair [%d]\n", opt->pen_unpaired);
 		fprintf(stderr, "       -x STR        read type. Setting -x changes multiple parameters unless overriden [null]\n");
 		fprintf(stderr, "                     pacbio: -k17 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -L0\n");
-		fprintf(stderr, "                     pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FeaD.001\n");
+		fprintf(stderr, "                     pbread: -k13 -W40 -w200 -c1000 -r10 -A2 -B5 -O2 -E1 -N25 -FVeaD.001\n");
 		fprintf(stderr, "\nInput/output options:\n\n");
 		fprintf(stderr, "       -p            first query file consists of interleaved paired-end sequences\n");
 		fprintf(stderr, "       -R STR        read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
@@ -182,11 +183,12 @@ int main_mem(int argc, char *argv[])
 			if (opt0.split_factor == 0.) opt->split_factor = 10.;
 			if (!opt0.min_chain_weight) opt->min_chain_weight = 40;
 			if (strcmp(mode, "pbread1") == 0 || strcmp(mode, "pbread") == 0) {
-				opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG;
+				opt->flag |= MEM_F_ALL | MEM_F_SELF_OVLP | MEM_F_ALN_REG | MEM_F_MERGE_REG;
 				if (!opt0.min_seed_len) opt->min_seed_len = 13;
 				if (!opt0.max_chain_extend) opt->max_chain_extend = 25;
 				if (opt0.drop_ratio == 0.) opt->drop_ratio = .001;
 			} else {
+				opt->flag |= MEM_F_MERGE_REG;
 				if (!opt0.min_seed_len) opt->min_seed_len = 17;
 				if (!opt0.pen_clip5) opt->pen_clip5 = 0;
 				if (!opt0.pen_clip3) opt->pen_clip3 = 0;
diff --git a/main.c b/main.c
index e2f9266..38cfa1a 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.8-r716-dirty"
+#define PACKAGE_VERSION "0.7.8-r718-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);