diff --git a/bwamem.c b/bwamem.c
index 9950097..6c59f59 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -712,7 +712,7 @@ mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *
 }
 
 // This routine is only used for the API purpose
-mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, const mem_alnreg_t *ar)
+mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, uint8_t *query, const mem_alnreg_t *ar)
 {
 	mem_aln_t a;
 	int qb = ar->qb, qe = ar->qe, NM, score, is_rev;
@@ -722,6 +722,18 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
 	bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re);
 	a.cigar = bwa_gen_cigar(opt->mat, opt->q, opt->r, opt->w, bns->l_pac, pac, qe - qb, (uint8_t*)&query[qb], rb, re, &score, &a.n_cigar, &NM);
 	a.NM = NM;
+	if (qb != 0 || qe != l_query) { // add clipping to CIGAR
+		int clip5, clip3;
+		clip5 = is_rev? l_query - qe : qb;
+		clip3 = is_rev? qb : l_query - qe;
+		a.cigar = realloc(a.cigar, 4 * (a.n_cigar + 2));
+		if (clip5) {
+			memmove(a.cigar+1, a.cigar, a.n_cigar * 4);
+			a.cigar[0] = clip5<<4|3;
+			++a.n_cigar;
+		}
+		if (clip3) a.cigar[a.n_cigar++] = clip3<<4|3;
+	}
 	pos = bns_depos(bns, rb < bns->l_pac? rb : re - 1, &is_rev);
 	a.is_rev = is_rev;
 	a.rid = bns_pos2rid(bns, pos);
diff --git a/bwamem.h b/bwamem.h
index 9996f6b..c2f124c 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -122,7 +122,7 @@ extern "C" {
 	 */
 	mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq);
 
-	mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, const mem_alnreg_t *ar);
+	mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, uint8_t *query, const mem_alnreg_t *ar);
 
 	/**
 	 * Infer the insert size distribution from interleaved alignment regions
diff --git a/example.c b/example.c
index 2fefde4..c0fede6 100644
--- a/example.c
+++ b/example.c
@@ -32,7 +32,7 @@ int main(int argc, char *argv[])
 		for (i = 0; i < ar.n; ++i) { // traverse each hit
 			mem_aln_t a;
 			if (ar.a[i].secondary >= 0) continue; // skip secondary alignments
-			a = mem_reg2aln(opt, idx->bns, idx->pac, (uint8_t*)ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR
+			a = mem_reg2aln(opt, idx->bns, idx->pac, ks->seq.l, (uint8_t*)ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR
 			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);
 			for (k = 0; k < a.n_cigar; ++k)
 				printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]);
diff --git a/main.c b/main.c
index 0009fc6..d301bb4 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.2-r308-beta"
+#define PACKAGE_VERSION "0.6.2-r309-beta"
 #endif
 
 static int usage()