diff --git a/bwtsw2.h b/bwtsw2.h
index 8354511..c156c31 100644
--- a/bwtsw2.h
+++ b/bwtsw2.h
@@ -13,7 +13,7 @@
 
 typedef struct {
 	int a, b, q, r, t, qr, bw;
-	int z, is, t_seeds, hard_clip;
+	int z, is, t_seeds, hard_clip, multi_2nd;
 	float mask_level, coef;
 	int n_threads, chunk_size;
 } bsw2opt_t;
diff --git a/bwtsw2_main.c b/bwtsw2_main.c
index 34d3822..ff5595a 100644
--- a/bwtsw2_main.c
+++ b/bwtsw2_main.c
@@ -17,7 +17,7 @@ int bwa_bwtsw2(int argc, char *argv[])
 
 	opt = bsw2_init_opt();
 	srand48(11);
-	while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:")) >= 0) {
+	while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:M")) >= 0) {
 		switch (c) {
 		case 'q': opt->q = atoi(optarg); break;
 		case 'r': opt->r = atoi(optarg); break;
@@ -31,6 +31,7 @@ int bwa_bwtsw2(int argc, char *argv[])
 		case 'm': opt->mask_level = atof(optarg); break;
 		case 'c': opt->coef = atof(optarg); break;
 		case 'N': opt->t_seeds = atoi(optarg); break;
+		case 'M': opt->multi_2nd = 1; break;
 		case 'H': opt->hard_clip = 1; break;
 		case 'f': xreopen(optarg, "w", stdout); break;
 		}
@@ -44,19 +45,20 @@ int bwa_bwtsw2(int argc, char *argv[])
 		fprintf(stderr, "         -b INT   mismatch penalty [%d]\n", opt->b);
 		fprintf(stderr, "         -q INT   gap open penalty [%d]\n", opt->q);
 		fprintf(stderr, "         -r INT   gap extension penalty [%d]\n", opt->r);
-		fprintf(stderr, "\n");
-		fprintf(stderr, "         -t INT   number of threads [%d]\n", opt->n_threads);
-		fprintf(stderr, "\n");
 		fprintf(stderr, "         -w INT   band width [%d]\n", opt->bw);
 		fprintf(stderr, "         -m FLOAT mask level [%.2f]\n", opt->mask_level);
 		fprintf(stderr, "\n");
+		fprintf(stderr, "         -t INT   number of threads [%d]\n", opt->n_threads);
+        fprintf(stderr, "         -f FILE  file to output results to instead of stdout\n");
+		fprintf(stderr, "         -H       in SAM output, use hard clipping instead of soft clipping\n");
+		fprintf(stderr, "         -M       mark multi-part alignments as secondary\n");
+		fprintf(stderr, "\n");
 		fprintf(stderr, "         -T INT   score threshold divided by a [%d]\n", opt->t);
-		fprintf(stderr, "         -s INT   maximum seeding interval size [%d]\n", opt->is);
-		fprintf(stderr, "         -z INT   Z-best [%d]\n", opt->z);
-		fprintf(stderr, "         -N INT   # seeds to trigger reverse alignment [%d]\n", opt->t_seeds);
 		fprintf(stderr, "         -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef);
-		fprintf(stderr, "         -H       in SAM output, use hard clipping rather than soft\n");
-        fprintf(stderr, "         -f FILE  file to output results to instead of stdout\n\n");
+		fprintf(stderr, "         -z INT   Z-best [%d]\n", opt->z);
+		fprintf(stderr, "         -s INT   maximum seeding interval size [%d]\n", opt->is);
+		fprintf(stderr, "         -N INT   # seeds to trigger reverse alignment [%d]\n", opt->t_seeds);
+		fprintf(stderr, "\n");
 		fprintf(stderr, "Note: For long Illumina, 454 and Sanger reads, assembly contigs, fosmids and\n");
 		fprintf(stderr, "      BACs, the default setting usually works well. For the current PacBio\n");
 		fprintf(stderr, "      reads (end of 2010), '-b5 -q2 -r1 -z10' is recommended. One may also\n");