added fread return value checking and associated error messages.

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;
        }
-       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));     
-       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));
@@ -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
-               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) {
-                       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);
-                       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);
-                       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) {
@@ -368,11 +392,19 @@ static bam_index_t *bam_index_load_core(FILE *fp)
                        }
                }
                // 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);
-               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]);
        }