diff --git a/bntseq.c b/bntseq.c
index 6589434..465e383 100644
--- a/bntseq.c
+++ b/bntseq.c
@@ -179,17 +179,25 @@ bntseq_t *bns_restore(const char *prefix)
 	if ((fp = fopen(strcat(strcpy(alt_filename, prefix), ".alt"), "r")) != 0) { // read .alt file if present
 		char str[1024];
 		khash_t(str) *h;
-		int i, absent;
+		int c, i, absent;
 		khint_t k;
 		h = kh_init(str);
 		for (i = 0; i < bns->n_seqs; ++i) {
 			k = kh_put(str, h, bns->anns[i].name, &absent);
 			kh_val(h, k) = i;
 		}
-		while (fscanf(fp, "%s", str) == 1) {
-			k = kh_get(str, h, str);
-			if (k != kh_end(h))
-				bns->anns[kh_val(h, k)].is_alt = 1;
+		i = 0;
+		while ((c = fgetc(fp)) != EOF) {
+			if (c == '\t' || c == '\n' || c == '\r') {
+				str[i] = 0;
+				if (str[0] != '@') {
+					k = kh_get(str, h, str);
+					if (k != kh_end(h))
+						bns->anns[kh_val(h, k)].is_alt = 1;
+				}
+				while (c != '\n' && c != EOF) c = fgetc(fp);
+				i = 0;
+			} else str[i++] = c; // FIXME: potential segfault here
 		}
 		kh_destroy(str, h);
 		fclose(fp);
diff --git a/bwa.c b/bwa.c
index 43d8a58..495b197 100644
--- a/bwa.c
+++ b/bwa.c
@@ -239,7 +239,12 @@ bwaidx_t *bwa_idx_load(const char *hint, int which)
 	idx = calloc(1, sizeof(bwaidx_t));
 	if (which & BWA_IDX_BWT) idx->bwt = bwa_idx_load_bwt(hint);
 	if (which & BWA_IDX_BNS) {
+		int i, c;
 		idx->bns = bns_restore(prefix);
+		for (i = c = 0; i < idx->bns->n_seqs; ++i)
+			if (idx->bns->anns[i].is_alt) ++c;
+		if (bwa_verbose >= 3)
+			fprintf(stderr, "[M::%s] read %d ALT contigs\n", __func__, c);
 		if (which & BWA_IDX_PAC) {
 			idx->pac = calloc(idx->bns->l_pac/4+1, 1);
 			err_fread_noeof(idx->pac, 1, idx->bns->l_pac/4+1, idx->bns->fp_pac); // concatenated 2-bit encoded sequence
diff --git a/main.c b/main.c
index db3c34f..77cace1 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r895-dirty"
+#define PACKAGE_VERSION "0.7.10-r896-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);