diff --git a/bwamem.c b/bwamem.c
index a10448a..71eb436 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -837,7 +837,7 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
 	}
 	a.rid = bns_pos2rid(bns, pos);
 	a.pos = pos - bns->anns[a.rid].offset;
-	a.score = ar->score; a.sub = ar->sub;
+	a.score = ar->score; a.sub = ar->sub > ar->csub? ar->sub : ar->csub;
 	free(query);
 	return a;
 }
diff --git a/bwamem_pair.c b/bwamem_pair.c
index 5f2c7bb..6316f6a 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -295,6 +295,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 		h[1] = mem_reg2aln(opt, bns, pac, s[1].l_seq, s[1].seq, &a[1].a[z[1]]); h[1].mapq = q_se[1]; h[1].flag |= 0x80 | extra_flag;
 		mem_aln2sam(bns, &str, &s[0], 1, &h[0], 0, &h[1]); s[0].sam = strdup(str.s); str.l = 0;
 		mem_aln2sam(bns, &str, &s[1], 1, &h[1], 0, &h[0]); s[1].sam = str.s;
+		free(h[0].cigar); free(h[1].cigar);
 	} else goto no_pairing;
 	return n;
 
@@ -306,5 +307,6 @@ no_pairing:
 	}
 	mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]);
 	mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]);
+	free(h[0].cigar); free(h[1].cigar);
 	return n;
 }
diff --git a/example.c b/example.c
index b59eec2..7c25674 100644
--- a/example.c
+++ b/example.c
@@ -34,7 +34,7 @@ int main(int argc, char *argv[])
 			if (ar.a[i].secondary >= 0) continue; // skip secondary alignments
 			a = mem_reg2aln(opt, idx->bns, idx->pac, ks->seq.l, ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR
 			// print alignment
-			printf("%s\t%c\t%s\t%d\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, a.pos, a.mapq);
+			printf("%s\t%c\t%s\t%ld\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, (long)a.pos, a.mapq);
 			for (k = 0; k < a.n_cigar; ++k) // print CIGAR
 				printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]);
 			printf("\t%d\n", a.NM); // print edit distance
diff --git a/main.c b/main.c
index b0874f0..e6cb68d 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.2-r351"
+#define PACKAGE_VERSION "0.7.2-r359-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);