diff --git a/bwamem.h b/bwamem.h
index b7a4e79..40f47f8 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -16,6 +16,7 @@ typedef struct __smem_i smem_i;
 #define MEM_F_NOPAIRING 0x4
 #define MEM_F_ALL       0x8
 #define MEM_F_NO_MULTI  0x10
+#define MEM_F_NO_RESCUE 0x20
 
 typedef struct {
 	int a, b, q, r;         // match score, mismatch penalty and gap open/extension penalty. A gap of size k costs q+k*r
diff --git a/bwamem_pair.c b/bwamem_pair.c
index 23c99ef..0f6ff08 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -235,20 +235,21 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 
 	int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1;
 	kstring_t str;
-	mem_alnreg_v b[2];
 	mem_aln_t h[2];
 
 	str.l = str.m = 0; str.s = 0;
-	// perform SW for the best alignment
-	kv_init(b[0]); kv_init(b[1]);
-	for (i = 0; i < 2; ++i)
-		for (j = 0; j < a[i].n; ++j)
-			if (a[i].a[j].score >= a[i].a[0].score  - opt->pen_unpaired)
-				kv_push(mem_alnreg_t, b[i], a[i].a[j]);
-	for (i = 0; i < 2; ++i)
-		for (j = 0; j < b[i].n && j < opt->max_matesw; ++j)
-			n += mem_matesw(opt, bns->l_pac, pac, pes, &b[i].a[j], s[!i].l_seq, (uint8_t*)s[!i].seq, &a[!i]);
-	free(b[0].a); free(b[1].a);
+	if (!(opt->flag & MEM_F_NO_RESCUE)) { // then perform SW for the best alignment
+		mem_alnreg_v b[2];
+		kv_init(b[0]); kv_init(b[1]);
+		for (i = 0; i < 2; ++i)
+			for (j = 0; j < a[i].n; ++j)
+				if (a[i].a[j].score >= a[i].a[0].score  - opt->pen_unpaired)
+					kv_push(mem_alnreg_t, b[i], a[i].a[j]);
+		for (i = 0; i < 2; ++i)
+			for (j = 0; j < b[i].n && j < opt->max_matesw; ++j)
+				n += mem_matesw(opt, bns->l_pac, pac, pes, &b[i].a[j], s[!i].l_seq, (uint8_t*)s[!i].seq, &a[!i]);
+		free(b[0].a); free(b[1].a);
+	}
 	mem_mark_primary_se(opt, a[0].n, a[0].a);
 	mem_mark_primary_se(opt, a[1].n, a[1].a);
 	if (opt->flag&MEM_F_NOPAIRING) goto no_pairing;
@@ -305,7 +306,7 @@ no_pairing:
 			h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[0]);
 		else h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, 0);
 	}
-	if (h[0].rid == h[1].rid && h[0].rid >= 0) { // if the top hits from the two ends constitute a proper pair, flag it.
+	if (!(opt->flag & MEM_F_NOPAIRING) && h[0].rid == h[1].rid && h[0].rid >= 0) { // if the top hits from the two ends constitute a proper pair, flag it.
 		int64_t dist;
 		int d;
 		d = mem_infer_dir(bns->l_pac, a[0].a[0].rb, a[1].a[0].rb, &dist);
diff --git a/fastmap.c b/fastmap.c
index eda06bb..98963c0 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -26,7 +26,7 @@ int main_mem(int argc, char *argv[])
 	void *ko = 0, *ko2 = 0;
 
 	opt = mem_opt_init();
-	while ((c = getopt(argc, argv, "paMCPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:")) >= 0) {
+	while ((c = getopt(argc, argv, "paMCSPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg);
 		else if (c == 'w') opt->w = atoi(optarg);
 		else if (c == 'A') opt->a = atoi(optarg);
@@ -42,6 +42,7 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'a') opt->flag |= MEM_F_ALL;
 		else if (c == 'p') opt->flag |= MEM_F_PE;
 		else if (c == 'M') opt->flag |= MEM_F_NO_MULTI;
+		else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE;
 		else if (c == 'c') opt->max_occ = atoi(optarg);
 		else if (c == 'd') opt->zdrop = atoi(optarg);
 		else if (c == 'v') bwa_verbose = atoi(optarg);
@@ -63,7 +64,8 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -r FLOAT   look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
 //		fprintf(stderr, "       -s INT     look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
 		fprintf(stderr, "       -c INT     skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
-		fprintf(stderr, "       -P         skip pairing; perform mate SW only\n");
+		fprintf(stderr, "       -S         skip mate rescue\n");
+		fprintf(stderr, "       -P         skip pairing; mate rescue performed unless -S also in use\n");
 		fprintf(stderr, "       -A INT     score for a sequence match [%d]\n", opt->a);
 		fprintf(stderr, "       -B INT     penalty for a mismatch [%d]\n", opt->b);
 		fprintf(stderr, "       -O INT     gap open penalty [%d]\n", opt->q);
diff --git a/main.c b/main.c
index 1104838..c9acc72 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.3-r372-beta"
+#define PACKAGE_VERSION "0.7.3-r373-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);