diff --git a/bwape.c b/bwape.c
index 4e94373..3336538 100644
--- a/bwape.c
+++ b/bwape.c
@@ -718,8 +718,14 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 
 		fprintf(stderr, "[bwa_sai2sam_pe_core] print alignments... ");
 		for (i = 0; i < n_seqs; ++i) {
-			bwa_print_sam1(bns, seqs[0] + i, seqs[1] + i, opt.mode, opt.max_top2);
-			bwa_print_sam1(bns, seqs[1] + i, seqs[0] + i, opt.mode, opt.max_top2);
+			bwa_seq_t *p[2];
+			p[0] = seqs[0] + i; p[1] = seqs[1] + i;
+			if (p[0]->bc[0] || p[1]->bc[0]) {
+				strcat(p[0]->bc, p[1]->bc);
+				strcpy(p[1]->bc, p[0]->bc);
+			}
+			bwa_print_sam1(bns, p[0], p[1], opt.mode, opt.max_top2);
+			bwa_print_sam1(bns, p[1], p[0], opt.mode, opt.max_top2);
 		}
 		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
 
diff --git a/main.c b/main.c
index 1b9d7f2..af5cc37 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "main.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.5.9rc1-r11"
+#define PACKAGE_VERSION "0.5.9rc1-r12"
 #endif
 
 static int usage()