diff --git a/NEWS.md b/NEWS.md
index fd42fa3..4692889 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,13 @@
+Release 0.7.12 (28 December 2014)
+---------------------------------
+
+This release fixed a bug in the pair-end mode when ALT contigs are present. It
+leads to undercalling in regions overlapping ALT contigs.
+
+(0.7.12: 28 December 2014, r1039)
+
+
+
 Release 0.7.11 (23 December, 2014)
 ----------------------------------
 
diff --git a/bwa.1 b/bwa.1
index 9b681b7..e30f382 100644
--- a/bwa.1
+++ b/bwa.1
@@ -1,4 +1,4 @@
-.TH bwa 1 "23 December 2014" "bwa-0.7.11-r1034" "Bioinformatics tools"
+.TH bwa 1 "23 December 2014" "bwa-0.7.12-r1034" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
diff --git a/bwamem_pair.c b/bwamem_pair.c
index f8b5d46..7950736 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -244,17 +244,6 @@ int mem_pair(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, cons
 
 void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m);
 
-static inline void mem_reg2sam_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, kstring_t *str, bseq1_t *s, mem_alnreg_t *p, int extra_flag, const mem_aln_t *m)
-{ // a simplified version of mem_reg2sam()
-	mem_aln_t t;
-	if (p->score < opt->T || p->secondary >= 0 || !p->is_alt) return;
-	t = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
-	t.flag |= extra_flag;
-	t.flag |= (opt->flag&MEM_F_NO_MULTI)? 0x10000 : 0x800;
-	mem_aln2sam(opt, bns, str, s, 1, &t, 0, m);
-	free(t.cigar);
-}
-
 #define raw_mapq(diff, a) ((int)(6.02 * (diff) / (a) + .499))
 
 int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2])
@@ -264,11 +253,14 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 	extern void mem_reg2sam(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m);
 	extern char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_alnreg_v *a, int l_query, const char *query);
 
-	int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1, n_pri[2];
+	int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1, n_pri[2], n_aa[2];
 	kstring_t str;
-	mem_aln_t h[2];
+	mem_aln_t h[2], g[2], aa[2][2];
 
 	str.l = str.m = 0; str.s = 0;
+	memset(h, 0, sizeof(mem_aln_t) * 2);
+	memset(g, 0, sizeof(mem_aln_t) * 2);
+	n_aa[0] = n_aa[1] = 0;
 	if (!(opt->flag & MEM_F_NO_RESCUE)) { // then perform SW for the best alignment
 		mem_alnreg_v b[2];
 		kv_init(b[0]); kv_init(b[1]);
@@ -324,38 +316,49 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 			q_se[0] = mem_approx_mapq_se(opt, &a[0].a[0]);
 			q_se[1] = mem_approx_mapq_se(opt, &a[1].a[0]);
 		}
-		// suboptimal hits
-		if (!(opt->flag & MEM_F_ALL)) {
-			for (i = 0; i < 2; ++i) {
-				int k = a[i].a[z[i]].secondary_all;
-				if (k >= 0 && k < n_pri[i]) { // switch secondary and primary if both of them are non-ALT
-					assert(a[i].a[k].secondary_all < 0);
-					for (j = 0; j < a[i].n; ++j)
-						if (a[i].a[j].secondary_all == k || j == k)
-							a[i].a[j].secondary_all = z[i];
-					a[i].a[z[i]].secondary_all = -1;
-				}
-				XA[i] = mem_gen_alt(opt, bns, pac, &a[i], s[i].l_seq, s[i].seq);
+		for (i = 0; i < 2; ++i) {
+			int k = a[i].a[z[i]].secondary_all;
+			if (k >= 0 && k < n_pri[i]) { // switch secondary and primary if both of them are non-ALT
+				assert(a[i].a[k].secondary_all < 0);
+				for (j = 0; j < a[i].n; ++j)
+					if (a[i].a[j].secondary_all == k || j == k)
+						a[i].a[j].secondary_all = z[i];
+				a[i].a[z[i]].secondary_all = -1;
 			}
+		}
+		if (!(opt->flag & MEM_F_ALL)) {
+			for (i = 0; i < 2; ++i)
+				XA[i] = mem_gen_alt(opt, bns, pac, &a[i], s[i].l_seq, s[i].seq);
 		} else XA[0] = XA[1] = 0;
 		// write SAM
-		h[0] = mem_reg2aln(opt, bns, pac, s[0].l_seq, s[0].seq, &a[0].a[z[0]]); h[0].mapq = q_se[0]; h[0].flag |= 0x40 | extra_flag; h[0].XA = XA[0]? XA[0][z[0]] : 0;
-		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; h[1].XA = XA[1]? XA[1][z[1]] : 0;
-		mem_aln2sam(opt, bns, &str, &s[0], 1, &h[0], 0, &h[1]); // write the primary hit for read1
-		if (n_pri[0] < a[0].n) mem_reg2sam_alt(opt, bns, pac, &str, &s[0], &a[0].a[n_pri[0]], 0x41|extra_flag, &h[1]);
+		for (i = 0; i < 2; ++i) {
+			h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[z[i]]);
+			h[i].mapq = q_se[i];
+			h[i].flag |= 0x40<<i | extra_flag;
+			h[i].XA = XA[i]? XA[i][z[i]] : 0;
+			aa[i][n_aa[i]++] = h[i];
+			if (n_pri[i] < a[i].n) { // the read has ALT hits
+				mem_alnreg_t *p = &a[i].a[n_pri[i]];
+				if (p->score < opt->T || p->secondary >= 0 || !p->is_alt) continue;
+				g[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, p);
+				g[i].flag |= 0x800 | 0x40<<i | extra_flag;
+				g[i].XA = XA[i]? XA[i][n_pri[i]] : 0;
+				aa[i][n_aa[i]++] = g[i];
+			}
+		}
+		for (i = 0; i < n_aa[0]; ++i)
+			mem_aln2sam(opt, bns, &str, &s[0], n_aa[0], aa[0], i, &h[1]); // write read1 hits
 		s[0].sam = strdup(str.s); str.l = 0;
-		mem_aln2sam(opt, bns, &str, &s[1], 1, &h[1], 0, &h[0]); // write the primary hit for read2
-		if (n_pri[1] < a[1].n) mem_reg2sam_alt(opt, bns, pac, &str, &s[1], &a[1].a[n_pri[1]], 0x81|extra_flag, &h[0]);
+		for (i = 0; i < n_aa[1]; ++i)
+			mem_aln2sam(opt, bns, &str, &s[1], n_aa[1], aa[1], i, &h[0]); // write read2 hits
 		s[1].sam = str.s;
 		if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
-		free(h[0].cigar); // h[0].XA will be freed in the following block
-		free(h[1].cigar);
-		// free XA
+		// free
 		for (i = 0; i < 2; ++i) {
-			if (XA[i]) {
-				for (j = 0; j < a[i].n; ++j) free(XA[i][j]);
-				free(XA[i]);
-			}
+			free(h[i].cigar); free(g[i].cigar);
+			if (XA[i] == 0) continue;
+			for (j = 0; j < a[i].n; ++j) free(XA[i][j]);
+			free(XA[i]);
 		}
 	} else goto no_pairing;
 	return n;
diff --git a/main.c b/main.c
index e157df6..9f776d4 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.11-r1034"
+#define PACKAGE_VERSION "0.7.12-r1039"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);