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fix deserialization of zero-length reference names

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This commit is contained in:
Ilya Kolpakov
2018-06-19 14:46:05 -04:00
committed by Heng Li
parent 57f37551f8
commit 408e098859
1 changed files with 13 additions and 6 deletions
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index.c
+13 -6
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@@ -420,9 +420,14 @@ void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
fwrite(MM_IDX_MAGIC, 1, 4, fp);
fwrite(x, 4, 5, fp);
for (i = 0; i < mi->n_seq; ++i) {
uint8_t l = mi->seq[i].name ? strlen(mi->seq[i].name) : 0;
fwrite(&l, 1, 1, fp);
fwrite(mi->seq[i].name, 1, l, fp);
if (mi->seq[i].name) {
uint8_t l = strlen(mi->seq[i].name);
fwrite(&l, 1, 1, fp);
fwrite(mi->seq[i].name, 1, l, fp);
} else {
uint8_t l = 0;
fwrite(&l, 1, 1, fp);
}
fwrite(&mi->seq[i].len, 4, 1, fp);
sum_len += mi->seq[i].len;
}
@@ -465,9 +470,11 @@ mm_idx_t *mm_idx_load(FILE *fp)
uint8_t l;
mm_idx_seq_t *s = &mi->seq[i];
fread(&l, 1, 1, fp);
s->name = (char*)kmalloc(mi->km, l + 1);
fread(s->name, 1, l, fp);
s->name[l] = 0;
if (l) {
s->name = (char*)kmalloc(mi->km, l + 1);
fread(s->name, 1, l, fp);
s->name[l] = 0;
}
fread(&s->len, 4, 1, fp);
s->offset = sum_len;
sum_len += s->len;