From 84fd13beed19b8300e1cc7dd75e931f04e9581e9 Mon Sep 17 00:00:00 2001 From: Henry Amrhein Date: Fri, 21 Dec 2012 16:53:23 -0800 Subject: [PATCH] wrapped fread and fwrite calls. added meaningful error messages. added comment at possible sandbagging incident for little-endian machines. --- bam_index.c | 91 ++++++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 73 insertions(+), 18 deletions(-) diff --git a/bam_index.c b/bam_index.c index e63146a..3574cbc 100644 --- a/bam_index.c +++ b/bam_index.c @@ -259,10 +259,16 @@ 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, "[bam_index_save] failed to write magic number.\n"); + abort(); + } if (bam_is_be) { uint32_t x = idx->n; - fwrite(bam_swap_endian_4p(&x), 4, 1, fp); + if (fwrite(bam_swap_endian_4p(&x), 4, 1, fp) < 1) { + fprintf(stderr, "[bam_index_save] failed to write n_ref.\n"); + abort(); + } } else fwrite(&idx->n, 4, 1, fp); for (i = 0; i < idx->n; ++i) { khash_t(i) *index = idx->index[i]; @@ -271,49 +277,91 @@ 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, "[bam_index_save] failed to write n_bin.\n"); + abort(); + } + } else if (fwrite(&size, 4, 1, fp) < 1) { + fprintf(stderr, "[bam_index_save] failed to write n_bin.\n"); + abort(); + } 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, "[bam_index_save] failed to write bin.\n"); + abort(); + } + x = p->n; + if (fwrite(bam_swap_endian_4p(&x), 4, 1, fp) < 1) { + fprintf(stderr, "[bam_index_save] failed to write n_chunk.\n"); + abort(); + } 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, "[bam_index_save] failed to write chunk pair.\n"); + abort(); + } + // hmmm...sandbagging PPC or reverting? 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 { - fwrite(&kh_key(index, k), 4, 1, fp); - fwrite(&p->n, 4, 1, fp); - fwrite(p->list, 16, p->n, fp); + if (fwrite(&kh_key(index, k), 4, 1, fp) < 1) { + fprintf(stderr, "[bam_index_save] failed to write bin.\n"); + abort(); + } + if (fwrite(&p->n, 4, 1, fp) < 1) { + fprintf(stderr, "[bam_index_save] failed to write n_chunk.\n"); + abort(); + } + if (fwrite(p->list, 16, p->n, fp) < p->n) { + fprintf(stderr, "[bam_index_save] failed to write chunk pair.\n"); + abort(); + } } } } // 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, "[bam_index_save] failed to write n_intv.\n"); + abort(); + } + } else if (fwrite(&index2->n, 4, 1, fp) < 1) { + fprintf(stderr, "[bam_index_save] failed to write n_intv.\n"); + abort(); + } 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, "[bam_index_save] failed to write ioffset.\n"); + abort(); + } 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, "[bam_index_save] failed to write ioffset.\n"); + abort(); + } } { // 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, "[bam_index_save] failed to write n_no_coor.\n"); + abort(); + } } fflush(fp); } @@ -378,7 +426,7 @@ static bam_index_t *bam_index_load_core(FILE *fp) if (bam_is_be) bam_swap_endian_4p(&p->n); p->m = p->n; p->list = (pair64_t*)malloc(p->m * 16); - if (fread(p->list, 16, p->n, fp) < 16) { + if (fread(p->list, 16, p->n, fp) < p->n) { fprintf(stderr, "[bam_index_load] read error while loading chunk pairs.\n"); fclose(fp); return 0; @@ -400,7 +448,8 @@ static bam_index_t *bam_index_load_core(FILE *fp) if (bam_is_be) bam_swap_endian_4p(&index2->n); index2->m = index2->n; index2->offset = (uint64_t*)calloc(index2->m, 8); - if (fread(index2->offset, index2->n, 8, fp) < 8) { + ret = fread(index2->offset, index2->n, 8, fp); + if ((ret > 0) && (ret < 8)) { fprintf(stderr, "[bam_index_load] read error while loading ioffset.\n"); fclose(fp); return 0; @@ -470,7 +519,13 @@ static void download_from_remote(const char *url) } buf = (uint8_t*)calloc(buf_size, 1); while ((l = knet_read(fp_remote, buf, buf_size)) != 0) - fwrite(buf, 1, l, fp); + if (fwrite(buf, 1, l, fp) < l) { + fprintf(stderr, "[download_from_remote] fail to write to destination file.\n"); + free(buf); + knet_close(fp_remote); + fclose(fp); + return; + } free(buf); fclose(fp); knet_close(fp_remote); -- 2.30.2