diff --git a/bwa.c b/bwa.c
index 4e2775f..8e99f18 100644
--- a/bwa.c
+++ b/bwa.c
@@ -24,6 +24,7 @@ struct bwa_idx_t {
 
 struct bwa_buf_t {
 	int max_buf;
+	bwa_pestat_t pes;
 	gap_stack_t *stack;
 	gap_opt_t *opt;
 	int *diff_tab;
@@ -152,16 +153,15 @@ static void compute_NM(const uint8_t *pac, uint64_t l_pac, uint8_t *seq, int64_t
 	}
 }
 
-bwa_aln_t bwa_sa2aln(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, uint64_t sa, int n_gaps)
+void bwa_sa2aln(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, uint64_t sa, int n_gaps, bwa_aln_t *aln)
 {
 	extern bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int len, int *strand);
 	extern bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const uint8_t *seq, bwtint_t *_pos, int ext, int *n_cigar, int is_end_correct);
 	int strand, seq_len, i, n_gap, n_mm;
 	uint64_t pos3, pac_pos;
 	uint8_t *s[2];
-	bwa_aln_t aln;
 
-	memset(&aln, 0, sizeof(bwa_aln_t));
+	memset(aln, 0, sizeof(bwa_aln_t));
 	seq_len = strlen(seq);
 	if (seq_len<<1 > buf->max_buf) {
 		buf->max_buf = seq_len<<1;
@@ -174,38 +174,41 @@ bwa_aln_t bwa_sa2aln(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, uint
 		s[0][i] = s[1][i] = nst_nt4_table[(int)seq[i]];
 	seq_reverse(seq_len, s[1], 1);
 	pac_pos = bwa_sa2pos(idx->bns, idx->bwt, sa, seq_len, &strand);
-	if (strand) aln.flag |= 16;
+	if (strand) aln->flag |= 16;
 	if (n_gaps) { // only for gapped alignment
 		int n_cigar;
 		bwa_cigar_t *cigar16;
 		cigar16 = bwa_refine_gapped_core(idx->bns->l_pac, idx->pac, seq_len, s[strand], &pac_pos, strand? n_gaps : -n_gaps, &n_cigar, 1);
-		aln.n_cigar = n_cigar;
-		aln.cigar = malloc(n_cigar * 4);
+		aln->n_cigar = n_cigar;
+		aln->cigar = malloc(n_cigar * 4);
 		for (i = 0, pos3 = pac_pos; i < n_cigar; ++i) {
 			int op = cigar16[i]>>14;
 			int len = cigar16[i]&0x3fff;
 			if (op == 3) op = 4; // the 16-bit CIGAR is different from the 32-bit CIGAR
-			aln.cigar[i] = len<<4 | op;
+			aln->cigar[i] = len<<4 | op;
 			if (op == 0 || op == 2) pos3 += len;
 		}
 		free(cigar16);
 	} else { // ungapped
-		aln.n_cigar = 1;
-		aln.cigar = malloc(4);
-		aln.cigar[0] = seq_len<<4 | 0;
+		aln->n_cigar = 1;
+		aln->cigar = malloc(4);
+		aln->cigar[0] = seq_len<<4 | 0;
 		pos3 = pac_pos + seq_len;
 	}
-	aln.n_n = bns_cnt_ambi(idx->bns, pac_pos, pos3 - pac_pos, &aln.ref_id);
-	aln.offset = pac_pos - idx->bns->anns[aln.ref_id].offset;
-	if (pos3 - idx->bns->anns[aln.ref_id].offset > idx->bns->anns[aln.ref_id].len) // read mapped beyond the end of a sequence
-		aln.flag |= 4; // read unmapped
-	compute_NM(idx->pac, idx->bns->l_pac, s[strand], pac_pos, aln.n_cigar, aln.cigar, &n_mm, &n_gap);
-	aln.n_mm = n_mm;
-	aln.n_gap = n_gap;
-	return aln;
+	aln->n_n = bns_cnt_ambi(idx->bns, pac_pos, pos3 - pac_pos, &aln->ref_id);
+	aln->offset = pac_pos - idx->bns->anns[aln->ref_id].offset;
+	if (pos3 - idx->bns->anns[aln->ref_id].offset > idx->bns->anns[aln->ref_id].len) // read mapped beyond the end of a sequence
+		aln->flag |= 4; // read unmapped
+	compute_NM(idx->pac, idx->bns->l_pac, s[strand], pac_pos, aln->n_cigar, aln->cigar, &n_mm, &n_gap);
+	aln->n_mm = n_mm;
+	aln->n_gap = n_gap;
 }
 
-bwa_one_t *bwa_se2(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, int gen_cigar)
+/************************
+ * Single-end alignment *
+ ************************/
+
+bwa_one_t *bwa_se(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, int gen_cigar)
 {
 	bwa_one_t *one;
 	int best, cnt, i, seq_len;
@@ -245,18 +248,25 @@ bwa_one_t *bwa_se2(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, int ge
 	one->mapQ = one->mapQs;
 	// compute CIGAR on request
 	one->one.ref_id = -1;
-	if (gen_cigar) one->one = bwa_sa2aln(idx, buf, seq, one->sa, one->which->n_gapo + one->which->n_gape);
+	if (gen_cigar) bwa_sa2aln(idx, buf, seq, one->sa, one->which->n_gapo + one->which->n_gape, &one->one);
 	return one;
 }
 
-bwa_one_t *bwa_se(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq)
-{
-	return bwa_se2(idx, buf, seq, 1);
-}
-
 void bwa_one_destroy(bwa_one_t *one)
 {
 	free(one->sai.sai);
 	free(one->one.cigar);
 	free(one);
 }
+
+/************************
+ * Paired-end alignment *
+ ************************/
+
+void bwa_pestat(bwa_buf_t *buf, int n, bwa_one_t **o[2])
+{
+}
+
+void bwa_pe(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq[2], bwa_one_t *o[2])
+{
+}
diff --git a/bwa.h b/bwa.h
index 5a75c13..e8172da 100644
--- a/bwa.h
+++ b/bwa.h
@@ -55,6 +55,11 @@ typedef struct {
 	bwa_aln_t one;
 } bwa_one_t;
 
+typedef struct {
+	double avg, std, ap_prior;
+	uint64_t low, high, high_bayesian;
+} bwa_pestat_t;
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -89,9 +94,9 @@ extern "C" {
 	 *
 	 * @return        An alignment
 	 */
-	bwa_aln_t bwa_sa2aln(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, uint64_t sa, int n_gaps);
+	void bwa_sa2aln(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, uint64_t sa, int n_gaps, bwa_aln_t *aln);
 
-	bwa_one_t *bwa_se(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq);
+	bwa_one_t *bwa_se(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, int gen_cigar);
 
 	void bwa_one_destroy(bwa_one_t *one);