From: Henry Amrhein Date: Wed, 2 Jan 2013 20:35:14 +0000 (-0800) Subject: bam_index.c: X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=commitdiff_plain;h=5d2c0d15df64246aa55b086fa85f9c68ae27e402 bam_index.c: wrapped fread() and fwrite() calls with error checking removed unused and duplicated endian-swap after writing n-chunks for big-endian systems in bam_index_save() --- diff --git a/bam_index.c b/bam_index.c index 9610a26..8dc7ce3 100644 --- a/bam_index.c +++ b/bam_index.c @@ -259,11 +259,23 @@ void bam_index_save(const bam_index_t *idx, FILE *fp) { int32_t i, size; khint_t k; - fwrite("BAI\1", 1, 4, fp); + if (fwrite("BAI\1", 1, 4, fp) < 4) { + fprintf(stderr, "[%s] failed to write magic number.\n", __func__); + return; + } if (bam_is_be) { uint32_t x = idx->n; - fwrite(bam_swap_endian_4p(&x), 4, 1, fp); - } else fwrite(&idx->n, 4, 1, fp); + if (fwrite(bam_swap_endian_4p(&x), 4, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write n_ref.\n", __func__); + return; + } + } + else { + if (fwrite(&idx->n, 4, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write n_ref.\n", __func__); + return; + } + } for (i = 0; i < idx->n; ++i) { khash_t(i) *index = idx->index[i]; bam_lidx_t *index2 = idx->index2 + i; @@ -271,49 +283,100 @@ void bam_index_save(const bam_index_t *idx, FILE *fp) size = kh_size(index); if (bam_is_be) { // big endian uint32_t x = size; - fwrite(bam_swap_endian_4p(&x), 4, 1, fp); - } else fwrite(&size, 4, 1, fp); + if (fwrite(bam_swap_endian_4p(&x), 4, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write n_bin.\n", __func__); + return; + } + } + else { + if (fwrite(&size, 4, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write n_bin.\n", __func__); + return; + } + } for (k = kh_begin(index); k != kh_end(index); ++k) { if (kh_exist(index, k)) { bam_binlist_t *p = &kh_value(index, k); if (bam_is_be) { // big endian uint32_t x; - x = kh_key(index, k); fwrite(bam_swap_endian_4p(&x), 4, 1, fp); - x = p->n; fwrite(bam_swap_endian_4p(&x), 4, 1, fp); + x = kh_key(index, k); + if (fwrite(bam_swap_endian_4p(&x), 4, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write bin.\n", __func__); + return; + } + x = p->n; + if (fwrite(bam_swap_endian_4p(&x), 4, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write n_chunk.\n", __func__); + return; + } for (x = 0; (int)x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); } - fwrite(p->list, 16, p->n, fp); + if (fwrite(p->list, 16, p->n, fp) < p->n) { + fprintf(stderr, "[%s] failed to write %d chunks.\n", __func__, p->n); + return; + } + /* for (x = 0; (int)x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); + } */ + } + else { + if (fwrite(&kh_key(index, k), 4, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write bin.\n", __func__); + return; + } + if (fwrite(&p->n, 4, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write n_chunk.\n", __func__); + return; + } + if (fwrite(p->list, 16, p->n, fp) < p->n) { + fprintf(stderr, "[%s] failed to write %d chunks.\n", __func__, p->n); + return; } - } else { - fwrite(&kh_key(index, k), 4, 1, fp); - fwrite(&p->n, 4, 1, fp); - fwrite(p->list, 16, p->n, fp); } } } // write linear index (index2) if (bam_is_be) { int x = index2->n; - fwrite(bam_swap_endian_4p(&x), 4, 1, fp); - } else fwrite(&index2->n, 4, 1, fp); + if (fwrite(bam_swap_endian_4p(&x), 4, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write n_intv.\n", __func__); + return; + } + } + else { + if (fwrite(&index2->n, 4, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write n_intv.\n", __func__); + return; + } + } if (bam_is_be) { // big endian int x; for (x = 0; (int)x < index2->n; ++x) bam_swap_endian_8p(&index2->offset[x]); - fwrite(index2->offset, 8, index2->n, fp); + if (fwrite(index2->offset, 8, index2->n, fp) < index2->n) { + fprintf(stderr, "[%s] failed to write ioffset.\n", __func__); + return; + } for (x = 0; (int)x < index2->n; ++x) bam_swap_endian_8p(&index2->offset[x]); - } else fwrite(index2->offset, 8, index2->n, fp); + } + else { + if (fwrite(index2->offset, 8, index2->n, fp) < index2->n) { + fprintf(stderr, "[%s] failed to write ioffset.\n", __func__); + return; + } + } } { // write the number of reads coor-less records. uint64_t x = idx->n_no_coor; if (bam_is_be) bam_swap_endian_8p(&x); - fwrite(&x, 8, 1, fp); + if (fwrite(&x, 8, 1, fp) < 1) { + fprintf(stderr, "[%s] failed to write n_no_coor.\n", __func__); + } } fflush(fp); } @@ -327,14 +390,22 @@ 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, "[%s] failed to read magic number.\n", __func__); + 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, "[%s] failed to read n_ref.\n", __func__); + 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 +418,34 @@ 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, "[%s] failed to read n_bin.\n", __func__); + 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, "[%s] failed to read bin.\n", __func__); + 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, "[%s] failed to read n_chunk.\n", __func__); + 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) < p->n) { + fprintf(stderr, "[%s] failed to read %d chunks.\n", __func__, p->n); + fclose(fp); + return 0; + } if (bam_is_be) { int x; for (x = 0; x < p->n; ++x) { @@ -368,13 +455,26 @@ 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, "[%s] failed to read n_intv", __func__); + 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 (bam_is_be) - for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]); + if (index2->n > 0) { + index2->m = index2->n; + index2->offset = (uint64_t*)calloc(index2->m, 8); + if (fread(index2->offset, index2->n, 8, fp) < index2->n) { + fprintf(stderr, "[%s] failed to read %d intervals.", __func__, index2->n); + fclose(fp); + return 0; + } + if (bam_is_be) { + for (j = 0; j < index2->n; ++j) { + bam_swap_endian_8p(&index2->offset[j]); + } + } + } } if (fread(&idx->n_no_coor, 8, 1, fp) == 0) idx->n_no_coor = 0; if (bam_is_be) bam_swap_endian_8p(&idx->n_no_coor); @@ -437,8 +537,12 @@ static void download_from_remote(const char *url) return; } buf = (uint8_t*)calloc(buf_size, 1); - while ((l = knet_read(fp_remote, buf, buf_size)) != 0) - fwrite(buf, 1, l, fp); + while ((l = knet_read(fp_remote, buf, buf_size)) != 0) { + if (fwrite(buf, 1, l, fp) < l) { + fprintf(stderr, "[%s] fail to write to destination file.\n", __func__); + break; + } + } free(buf); fclose(fp); knet_close(fp_remote);