From: Henry Amrhein <hamrhein@caltech.edu>
Date: Fri, 21 Dec 2012 20:32:49 +0000 (-0800)
Subject: added fread return value checking and associated error messages.
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=commitdiff_plain;h=2b0bb2474587f6e2f2c03c34c3f5882905c60bcc

added fread return value checking and associated error messages.
---

diff --git a/bam_index.c b/bam_index.c
index 9610a26..e63146a 100644
--- 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]);
 	}