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1056316
)
added fread return value checking and associated error messages.
author
Henry Amrhein
<hamrhein@caltech.edu>
Fri, 21 Dec 2012 20:32:49 +0000
(12:32 -0800)
committer
Henry Amrhein
<hamrhein@caltech.edu>
Fri, 21 Dec 2012 20:32:49 +0000
(12:32 -0800)
bam_index.c
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diff --git
a/bam_index.c
b/bam_index.c
index 9610a2656031657b796abc68bf32c1b6f1564745..e63146af20670ce7eb3ea940ac47f50c92b9e86b 100644
(file)
--- a/
bam_index.c
+++ b/
bam_index.c
@@
-327,14
+327,22
@@
static bam_index_t *bam_index_load_core(FILE *fp)
fprintf(stderr, "[bam_index_load_core] fail to load index.\n");
return 0;
}
fprintf(stderr, "[bam_index_load_core] fail to load index.\n");
return 0;
}
- fread(magic, 1, 4, fp);
+ if (fread(magic, 1, 4, fp) < 4) {
+ fprintf(stderr, "[bam_index_load] failed to read magic number.\n");
+ fclose(fp);
+ return 0;
+ }
if (strncmp(magic, "BAI\1", 4)) {
fprintf(stderr, "[bam_index_load] wrong magic number.\n");
fclose(fp);
return 0;
}
idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
if (strncmp(magic, "BAI\1", 4)) {
fprintf(stderr, "[bam_index_load] wrong magic number.\n");
fclose(fp);
return 0;
}
idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
- fread(&idx->n, 4, 1, fp);
+ if (fread(&idx->n, 4, 1, fp) < 1) {
+ fprintf(stderr, "[bam_index_load] failed to read n_ref field.\n");
+ fclose(fp);
+ return 0;
+ }
if (bam_is_be) bam_swap_endian_4p(&idx->n);
idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
if (bam_is_be) bam_swap_endian_4p(&idx->n);
idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
@@
-347,18
+355,34
@@
static bam_index_t *bam_index_load_core(FILE *fp)
bam_binlist_t *p;
index = idx->index[i] = kh_init(i);
// load binning index
bam_binlist_t *p;
index = idx->index[i] = kh_init(i);
// load binning index
- fread(&size, 4, 1, fp);
+ if (fread(&size, 4, 1, fp) < 1) {
+ fprintf(stderr, "[bam_index_load] read error while loading n_bin.\n");
+ fclose(fp);
+ return 0;
+ }
if (bam_is_be) bam_swap_endian_4p(&size);
for (j = 0; j < (int)size; ++j) {
if (bam_is_be) bam_swap_endian_4p(&size);
for (j = 0; j < (int)size; ++j) {
- fread(&key, 4, 1, fp);
+ if (fread(&key, 4, 1, fp) < 1) {
+ fprintf(stderr, "[bam_index_load] read error while loading bin.\n");
+ fclose(fp);
+ return 0;
+ }
if (bam_is_be) bam_swap_endian_4p(&key);
k = kh_put(i, index, key, &ret);
p = &kh_value(index, k);
if (bam_is_be) bam_swap_endian_4p(&key);
k = kh_put(i, index, key, &ret);
p = &kh_value(index, k);
- fread(&p->n, 4, 1, fp);
+ if (fread(&p->n, 4, 1, fp) < 1) {
+ fprintf(stderr, "[bam_index_load] read error while loading n_chunk.\n");
+ fclose(fp);
+ return 0;
+ }
if (bam_is_be) bam_swap_endian_4p(&p->n);
p->m = p->n;
p->list = (pair64_t*)malloc(p->m * 16);
if (bam_is_be) bam_swap_endian_4p(&p->n);
p->m = p->n;
p->list = (pair64_t*)malloc(p->m * 16);
- fread(p->list, 16, p->n, fp);
+ if (fread(p->list, 16, p->n, fp) < 16) {
+ fprintf(stderr, "[bam_index_load] read error while loading chunk pairs.\n");
+ fclose(fp);
+ return 0;
+ }
if (bam_is_be) {
int x;
for (x = 0; x < p->n; ++x) {
if (bam_is_be) {
int x;
for (x = 0; x < p->n; ++x) {
@@
-368,11
+392,19
@@
static bam_index_t *bam_index_load_core(FILE *fp)
}
}
// load linear index
}
}
// load linear index
- fread(&index2->n, 4, 1, fp);
+ if (fread(&index2->n, 4, 1, fp) < 1) {
+ fprintf(stderr, "[bam_index_load] read error while loading n_intv.\n");
+ fclose(fp);
+ return 0;
+ }
if (bam_is_be) bam_swap_endian_4p(&index2->n);
index2->m = index2->n;
index2->offset = (uint64_t*)calloc(index2->m, 8);
if (bam_is_be) bam_swap_endian_4p(&index2->n);
index2->m = index2->n;
index2->offset = (uint64_t*)calloc(index2->m, 8);
- fread(index2->offset, index2->n, 8, fp);
+ if (fread(index2->offset, index2->n, 8, fp) < 8) {
+ fprintf(stderr, "[bam_index_load] read error while loading ioffset.\n");
+ fclose(fp);
+ return 0;
+ }
if (bam_is_be)
for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
}
if (bam_is_be)
for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
}