diff --git a/index.c b/index.c
index 4b92fe6..533394c 100644
--- a/index.c
+++ b/index.c
@@ -31,6 +31,16 @@ typedef struct mm_idx_bucket_s {
 	void *h;     // hash table indexing _p_ and minimizers appearing once
 } mm_idx_bucket_t;
 
+typedef struct {
+	int32_t st, en, max; // max is not used for now
+	int32_t score:30, strand:2;
+} mm_idx_intv1_t;
+
+typedef struct mm_idx_intv_s {
+	int32_t n, m;
+	mm_idx_intv1_t *a;
+} mm_idx_intv_t;
+
 mm_idx_t *mm_idx_init(int w, int k, int b, int flag)
 {
 	mm_idx_t *mi;
@@ -55,6 +65,11 @@ void mm_idx_destroy(mm_idx_t *mi)
 			kh_destroy(idx, (idxhash_t*)mi->B[i].h);
 		}
 	}
+	if (mi->I) {
+		for (i = 0; i < mi->n_seq; ++i)
+			free(mi->I[i].a);
+		free(mi->I);
+	}
 	if (!mi->km) {
 		for (i = 0; i < mi->n_seq; ++i)
 			free(mi->seq[i].name);
@@ -592,16 +607,6 @@ int mm_idx_reader_eof(const mm_idx_reader_t *r) // TODO: in extremely rare cases
 #include "kseq.h"
 KSTREAM_DECLARE(gzFile, gzread)
 
-typedef struct {
-	int32_t st, en, max; // max is not used for now
-	int32_t score:30, strand:2;
-} mm_idx_intv1_t;
-
-typedef struct mm_idx_intv_s {
-	int32_t n, m;
-	mm_idx_intv1_t *a;
-} mm_idx_intv_t;
-
 #define sort_key_bed(a) ((a).st)
 KRADIX_SORT_INIT(bed, mm_idx_intv1_t, sort_key_bed, 4)
 
@@ -648,10 +653,11 @@ mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn)
 		r = &I[id];
 		if (r->n == r->m) {
 			r->m = r->m? r->m + (r->m>>1) : 16;
-			r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a));
+			r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
 		}
 		r->a[r->n++] = t;
 	}
+	free(str.s);
 	ks_destroy(ks);
 	gzclose(fp);
 	return I;
@@ -663,9 +669,9 @@ int mm_idx_bed_read(mm_idx_t *mi, const char *fn)
 	if (mi->h == 0) mm_idx_index_name(mi);
 	mi->I = mm_idx_read_bed(mi, fn);
 	if (mi->I == 0) return -1;
-	for (i = 0; i < mi->n_seq; ++i)
+	for (i = 0; i < mi->n_seq; ++i) // TODO: eliminate redundant intervals
 		radix_sort_bed(mi->I[i].a, mi->I[i].a + mi->I[i].n);
-	return mi->I? 0 : -1;
+	return 0;
 }
 
 int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s)
@@ -683,6 +689,7 @@ int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uin
 	}
 	for (i = left; i < r->n; ++i) {
 		if (st <= r->a[i].st && en >= r->a[i].en && r->a[i].strand != 0) {
+			//fprintf(stderr, "[2] %d\t%d\t%c\n", r->a[i].st, r->a[i].en, r->a[i].strand > 0? '+' : r->a[i].strand < 0? '-' : '.');
 			if (r->a[i].strand > 0) {
 				s[r->a[i].st] |= 1, s[r->a[i].en - 1] |= 2;
 			} else {
diff --git a/main.c b/main.c
index f7b529b..e2e7837 100644
--- a/main.c
+++ b/main.c
@@ -206,7 +206,7 @@ int main(int argc, char *argv[])
 		else if (c == 336) opt.flag |= MM_F_HARD_MLEVEL; // --hard-mask-level
 		else if (c == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
 		else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
-		else if (c == 339) junc_bed = o.arg; // --junc-bed
+		else if (c == 340) junc_bed = o.arg; // --junc-bed
 		else if (c == 314) { // --frag
 			yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
 		} else if (c == 315) { // --secondary
@@ -346,7 +346,6 @@ int main(int argc, char *argv[])
 	if (opt.best_n == 0 && (opt.flag&MM_F_CIGAR) && mm_verbose >= 2)
 		fprintf(stderr, "[WARNING]\033[1;31m `-N 0' reduces alignment accuracy. Please use --secondary=no to suppress secondary alignments.\033[0m\n");
 	while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
-		if (junc_bed) mm_idx_bed_read(mi, junc_bed);
 		if ((opt.flag & MM_F_CIGAR) && (mi->flag & MM_I_NO_SEQ)) {
 			fprintf(stderr, "[ERROR] the prebuilt index doesn't contain sequences.\n");
 			mm_idx_destroy(mi);
@@ -367,6 +366,7 @@ int main(int argc, char *argv[])
 					__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
 		if (argc != o.ind + 1) mm_mapopt_update(&opt, mi);
 		if (mm_verbose >= 3) mm_idx_stat(mi);
+		if (junc_bed) mm_idx_bed_read(mi, junc_bed);
 		if (!(opt.flag & MM_F_FRAG_MODE)) {
 			for (i = o.ind + 1; i < argc; ++i)
 				mm_map_file(mi, argv[i], &opt, n_threads);