wrapped fread and fwrite calls.

added meaningful error messages.
added comment at possible sandbagging incident for little-endian machines.

diff --git a/bam_index.c b/bam_index.c
index e63146af20670ce7eb3ea940ac47f50c92b9e86b..3574cbc230aeee9c06e88791e2db7ee16e27e438 100644 (file)
--- 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);