diff --git a/bwamem.c b/bwamem.c
index 4fffe38..ae1886a 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -554,7 +554,9 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
 		} else kputw(0, str);
 		kputc('\t', str);
 	} else kputsn("\t*\t0\t0\t", 7, str);
-	if (!(p->flag&0x10)) { // print SEQ and QUAL, the forward strand
+	if (p->flag&0x100) { // for secondary alignments, don't write SEQ and QUAL
+		kputsn("*\t*", 3, str);
+	} else if (!(p->flag&0x10)) { // print SEQ and QUAL, the forward strand
 		int i, qb = 0, qe = s->l_seq;
 		if (!(p->flag&4) && is_hard) qb = p->qb, qe = p->qe;
 		ks_resize(str, str->l + (qe - qb) + 1);
@@ -610,7 +612,7 @@ void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h)
 {
 	h->rb = a->rb; h->re = a->re; h->qb = a->qb; h->qe = a->qe;
 	h->score = a->score;
-	h->sub = a->sub > a->csub? a->sub : a->csub;
+	h->sub = a->secondary >= 0? -1 : a->sub > a->csub? a->sub : a->csub;
 	h->qual = 0; // quality unset
 	h->flag = a->secondary >= 0? 0x100 : 0; // only the "secondary" bit is set
 }
@@ -623,10 +625,10 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
 	if (a->n > 0) {
 		for (k = 0; k < a->n; ++k) {
 			bwahit_t h;
-			if (a->a[k].secondary >= 0) continue;
+			if (a->a[k].secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
 			mem_alnreg2hit(&a->a[k], &h);
 			h.flag |= extra_flag;
-			h.qual = mem_approx_mapq_se(opt, &a->a[k]);
+			h.qual = a->a[k].secondary >= 0? 0 : mem_approx_mapq_se(opt, &a->a[k]);
 			bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP, m);
 		}
 	} else bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, 0, opt->flag&MEM_F_HARDCLIP, m);
diff --git a/bwamem.h b/bwamem.h
index fa55b44..5cf3ac5 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -14,6 +14,7 @@ typedef struct __smem_i smem_i;
 #define MEM_F_HARDCLIP  0x1
 #define MEM_F_PE        0x2
 #define MEM_F_NOPAIRING 0x4
+#define MEM_F_ALL       0x8
 
 typedef struct {
 	int a, b, q, r, w;
diff --git a/fastmap.c b/fastmap.c
index 819e301..49c46fd 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -26,11 +26,12 @@ int main_mem(int argc, char *argv[])
 	void *ko = 0, *ko2 = 0;
 
 	opt = mem_opt_init();
-	while ((c = getopt(argc, argv, "CPHk:c:v:s:r:t:R:")) >= 0) {
+	while ((c = getopt(argc, argv, "aCPHk: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 == 'c') opt->max_occ = atoi(optarg);
 		else if (c == 'v') bwa_verbose = atoi(optarg);
 		else if (c == 'r') opt->split_factor = atof(optarg);
@@ -49,6 +50,9 @@ 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, "         -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         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");
 		fprintf(stderr, "\n");
 		free(opt);