diff --git a/fastmap.c b/fastmap.c
index a5cafd7..4cf92b2 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -26,12 +26,13 @@ int main_mem(int argc, char *argv[])
 	void *ko = 0, *ko2 = 0;
 
 	opt = mem_opt_init();
-	while ((c = getopt(argc, argv, "aCPHk:c:v:s:r:t:R:")) >= 0) {
+	while ((c = getopt(argc, argv, "paCPHk:c:v:s:r:t:R:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg);
 		else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
 		else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
 		else if (c == 'H') opt->flag |= MEM_F_HARDCLIP;
 		else if (c == 'a') opt->flag |= MEM_F_ALL;
+		else if (c == 'p') opt->flag |= MEM_F_PE;
 		else if (c == 'c') opt->max_occ = atoi(optarg);
 		else if (c == 'v') bwa_verbose = atoi(optarg);
 		else if (c == 'r') opt->split_factor = atof(optarg);
@@ -42,7 +43,7 @@ int main_mem(int argc, char *argv[])
 	}
 	if (optind + 1 >= argc) {
 		fprintf(stderr, "\n");
-		fprintf(stderr, "Usage:   bwa mem [options] <idxbase> <in.fq>\n\n");
+		fprintf(stderr, "Usage:   bwa mem [options] <idxbase> <in1.fq> [in2.fq]\n\n");
 		fprintf(stderr, "Options: -k INT     minimum seed length [%d]\n", opt->min_seed_len);
 		fprintf(stderr, "         -t INT     number of threads [%d]\n", opt->n_threads);
 		fprintf(stderr, "         -c INT     skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
@@ -51,6 +52,7 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "         -R STR     read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
 		fprintf(stderr, "         -v INT     verbose level [%d]\n", bwa_verbose);
 		fprintf(stderr, "         -a         output all alignments for SE or unpaired PE\n");
+		fprintf(stderr, "         -p         first query file consists of interleaved paired-end sequences\n");
 		fprintf(stderr, "         -P         perform mate SW only but skip pairing\n");
 		fprintf(stderr, "         -H         hard clipping\n");
 		fprintf(stderr, "         -C         append FASTA/FASTQ comment to SAM output\n");
@@ -58,6 +60,7 @@ int main_mem(int argc, char *argv[])
 		free(opt);
 		return 1;
 	}
+
 	mem_fill_scmat(opt->a, opt->b, opt->mat);
 	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
 	bwa_print_sam_hdr(idx->bns, rg_line);
@@ -66,10 +69,15 @@ int main_mem(int argc, char *argv[])
 	fp = gzdopen(fd, "r");
 	ks = kseq_init(fp);
 	if (optind + 2 < argc) {
-		ko2 = kopen(argv[optind + 2], &fd2);
-		fp2 = gzdopen(fd2, "r");
-		ks2 = kseq_init(fp2);
-		opt->flag |= MEM_F_PE;
+		if (opt->flag&MEM_F_PE) {
+			if (bwa_verbose >= 2)
+				fprintf(stderr, "[W::%s] when '-p' is in use, the second query file will be ignored.\n", __func__);
+		} else {
+			ko2 = kopen(argv[optind + 2], &fd2);
+			fp2 = gzdopen(fd2, "r");
+			ks2 = kseq_init(fp2);
+			opt->flag |= MEM_F_PE;
+		}
 	}
 	while ((seqs = bseq_read(opt->chunk_size * (ko2? 2 : 1), &n, ks, ks2)) != 0) {
 		int64_t size = 0;