From: Henry Amrhein <hamrhein@caltech.edu>
Date: Thu, 3 Jan 2013 06:16:32 +0000 (-0800)
Subject: bam_index.c:
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=commitdiff_plain;h=be7dd4a2678f3169a5616e0d74f153bba4928471

bam_index.c:
	added error checking for malloc(), calloc() and realloc() calls.
---

diff --git a/bam_index.c b/bam_index.c
index 8dc7ce3..c7f3395 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -80,11 +80,17 @@ static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t
 	l = &kh_value(h, k);
 	if (ret) { // not present
 		l->m = 1; l->n = 0;
-		l->list = (pair64_t*)calloc(l->m, 16);
+		if ((l->list = (pair64_t*)calloc(l->m, 16)) == NULL) {
+			fprintf(stderr, "[%s] failed to allocate bam_binlist node.\n", __func__);
+			abort();
+		}
 	}
 	if (l->n == l->m) {
 		l->m <<= 1;
-		l->list = (pair64_t*)realloc(l->list, l->m * 16);
+		if ((l->list = (pair64_t*)realloc(l->list, l->m * 16)) == NULL) {
+			fprintf(stderr, "[%s] failed to resize bam_binlist node.\n", __func__);
+			abort();
+		}
 	}
 	l->list[l->n].u = beg; l->list[l->n++].v = end;
 }
@@ -98,7 +104,10 @@ static inline void insert_offset2(bam_lidx_t *index2, bam1_t *b, uint64_t offset
 		int old_m = index2->m;
 		index2->m = end + 1;
 		kroundup32(index2->m);
-		index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
+		if ((index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8)) == NULL) {
+			fprintf(stderr, "[%s] failed to resize offset array.\n", __func__);
+			abort();
+		}
 		memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
 	}
 	if (beg == end) {
@@ -159,16 +168,34 @@ bam_index_t *bam_index_core(bamFile fp)
 	bam1_core_t *c;
 	uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
 
-	idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
-	b = (bam1_t*)calloc(1, sizeof(bam1_t));
+	if ((idx = (bam_index_t*)calloc(1, sizeof(bam_index_t))) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate bam_index structure.\n", __func__);
+		return NULL;
+	}
+	if ((b = (bam1_t*)calloc(1, sizeof(bam1_t))) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate bam1_t buffer.\n", __func__);
+		free(idx);
+		return NULL;
+	}
 	h = bam_header_read(fp);
 	c = &b->core;
 
 	idx->n = h->n_targets;
 	bam_header_destroy(h);
-	idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
+	if ((idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*))) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate bam_index bin hash.\n", __func__);
+		free(b);
+		free(idx);
+		return NULL;
+	}
 	for (i = 0; i < idx->n; ++i) idx->index[i] = kh_init(i);
-	idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
+	if ((idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t))) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate bam_index linear index.\n", __func__);
+		free(idx->index);
+		free(b);
+		free(idx);
+		return NULL;
+	}
 
 	save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
 	save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
@@ -400,15 +427,32 @@ static bam_index_t *bam_index_load_core(FILE *fp)
 		fclose(fp);
 		return 0;
 	}
-	idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));	
+	if ((idx = (bam_index_t*)calloc(1, sizeof(bam_index_t))) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate bam_index structure.\n", __func__);
+		fclose(fp);
+		return NULL;
+	}
 	if (fread(&idx->n, 4, 1, fp) < 1) {
 		fprintf(stderr, "[%s] failed to read n_ref.\n", __func__);
+		free(idx);
 		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));
+	if ((idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*))) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate bam_index bin hash.\n", __func__);
+		free(idx);
+		fclose(fp);
+		return NULL;
+	}
+	if ((idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t))) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate bam_index linear index.\n", __func__);
+		free(idx->index);
+		free(idx);
+		fclose(fp);
+		return NULL;
+	}
+
 	for (i = 0; i < idx->n; ++i) {
 		khash_t(i) *index;
 		bam_lidx_t *index2 = idx->index2 + i;
@@ -420,6 +464,8 @@ static bam_index_t *bam_index_load_core(FILE *fp)
 		// load binning index
 		if (fread(&size, 4, 1, fp) < 1) {
 			fprintf(stderr, "[%s] failed to read n_bin.\n", __func__);
+			free(idx->index);
+			free(idx);
 			fclose(fp);
 			return 0;
 		}
@@ -427,6 +473,8 @@ static bam_index_t *bam_index_load_core(FILE *fp)
 		for (j = 0; j < (int)size; ++j) {
 			if (fread(&key, 4, 1, fp) < 1) {
 				fprintf(stderr, "[%s] failed to read bin.\n", __func__);
+				free(idx->index);
+				free(idx);
 				fclose(fp);
 				return 0;
 			}
@@ -435,14 +483,24 @@ static bam_index_t *bam_index_load_core(FILE *fp)
 			p = &kh_value(index, k);
 			if (fread(&p->n, 4, 1, fp) < 1) {
 				fprintf(stderr, "[%s] failed to read n_chunk.\n", __func__);
+				free(idx->index);
+				free(idx);
 				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);
+			if ((p->list = (pair64_t*)malloc(p->m * 16)) == NULL) {
+				fprintf(stderr, "[%s] failed to allocate chunk array.\n", __func__);
+				free(idx->index);
+				free(idx);
+				fclose(fp);
+				return 0;
+			}
 			if (fread(p->list, 16, p->n, fp) < p->n) {
 				fprintf(stderr, "[%s] failed to read %d chunks.\n", __func__, p->n);
+				free(idx->index);
+				free(idx);
 				fclose(fp);
 				return 0;
 			}
@@ -457,15 +515,26 @@ static bam_index_t *bam_index_load_core(FILE *fp)
 		// load linear index
 		if (fread(&index2->n, 4, 1, fp) < 1) {
 			fprintf(stderr, "[%s] failed to read n_intv", __func__);
+			free(idx->index);
+			free(idx);
 			fclose(fp);
 			return 0;
 		}
 		if (bam_is_be) bam_swap_endian_4p(&index2->n);
 		if (index2->n > 0) {
 			index2->m = index2->n;
-			index2->offset = (uint64_t*)calloc(index2->m, 8);
+			if ((index2->offset = (uint64_t*)calloc(index2->m, 8)) == NULL) {
+				fprintf(stderr, "[%s] falied to allocate interval array.\n", __func__);
+				free(idx->index);
+				free(idx);
+				fclose(fp);
+				return 0;
+			}
 			if (fread(index2->offset, index2->n, 8, fp) < index2->n) {
 				fprintf(stderr, "[%s] failed to read %d intervals.", __func__, index2->n);
+				free(index2->offset);
+				free(idx->index);
+				free(idx);
 				fclose(fp);
 				return 0;
 			}
@@ -493,7 +562,11 @@ bam_index_t *bam_index_load_local(const char *_fn)
 			if (*p == '/') break;
 		fn = strdup(p + 1);
 	} else fn = strdup(_fn);
-	fnidx = (char*)calloc(strlen(fn) + 5, 1);
+	if ((fnidx = (char*)calloc(strlen(fn) + 5, 1)) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate space for index file name.\n", __func__);
+		free(fn);
+		return NULL;
+	}
 	strcpy(fnidx, fn); strcat(fnidx, ".bai");
 	fp = fopen(fnidx, "rb");
 	if (fp == 0) { // try "{base}.bai"
@@ -509,7 +582,11 @@ bam_index_t *bam_index_load_local(const char *_fn)
 		bam_index_t *idx = bam_index_load_core(fp);
 		fclose(fp);
 		return idx;
-	} else return 0;
+	}
+	else {
+		fprintf(stderr, "[%s] failed to open index file.\n", __func__);
+		return 0;
+	}
 }
 
 #ifdef _USE_KNETFILE
@@ -528,18 +605,22 @@ static void download_from_remote(const char *url)
 	++fn; // fn now points to the file name
 	fp_remote = knet_open(url, "r");
 	if (fp_remote == 0) {
-		fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
+		fprintf(stderr, "[%s] failed to open remote file.\n", __func__);
 		return;
 	}
 	if ((fp = fopen(fn, "wb")) == 0) {
-		fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
+		fprintf(stderr, "[%s] failed to create file in the working directory.\n", __func__);
 		knet_close(fp_remote);
 		return;
 	}
-	buf = (uint8_t*)calloc(buf_size, 1);
+	if ((buf = (uint8_t*)calloc(buf_size, 1)) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate buffer.\n", __func__);
+		fclose(fp);
+		return;
+	}
 	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__);
+			fprintf(stderr, "[%s] failed to write to destination file.\n", __func__);
 			break;
 		}
 	}
@@ -560,12 +641,16 @@ bam_index_t *bam_index_load(const char *fn)
 	idx = bam_index_load_local(fn);
 	if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) {
 		char *fnidx = calloc(strlen(fn) + 5, 1);
+		if (fnidx == NULL) {
+			fprintf(stderr, "[%s] failed to allocate space for index filename.\n", __func__);
+			return NULL;
+		}
 		strcat(strcpy(fnidx, fn), ".bai");
-		fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
+		fprintf(stderr, "[%s] attempting to download the remote index file.\n", __func__);
 		download_from_remote(fnidx);
 		idx = bam_index_load_local(fn);
 	}
-	if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
+	if (idx == 0) fprintf(stderr, "[%s] fail to load BAM index.\n", __func__);
 	return idx;
 }
 
@@ -576,13 +661,13 @@ int bam_index_build2(const char *fn, const char *_fnidx)
 	bamFile fp;
 	bam_index_t *idx;
 	if ((fp = bam_open(fn, "r")) == 0) {
-		fprintf(stderr, "[bam_index_build2] fail to open the BAM file.\n");
+		fprintf(stderr, "[%s] failure to open the BAM file.\n", __func__);
 		return -1;
 	}
 	idx = bam_index_core(fp);
 	bam_close(fp);
 	if(idx == 0) {
-		fprintf(stderr, "[bam_index_build2] fail to index the BAM file.\n");
+		fprintf(stderr, "[%s] fail to index the BAM file.\n", __func__);
 		return -1;
 	}
 	if (_fnidx == 0) {
@@ -591,7 +676,7 @@ int bam_index_build2(const char *fn, const char *_fnidx)
 	} else fnidx = strdup(_fnidx);
 	fpidx = fopen(fnidx, "wb");
 	if (fpidx == 0) {
-		fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
+		fprintf(stderr, "[%s] fail to create the index file.\n", __func__);
 		free(fnidx);
 		return -1;
 	}
@@ -693,17 +778,23 @@ bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
 	if (beg < 0) beg = 0;
 	if (end < beg) return 0;
 	// initialize iter
-	iter = calloc(1, sizeof(struct __bam_iter_t));
+	if ((iter = calloc(1, sizeof(struct __bam_iter_t))) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate bam iterator.\n", __func__);
+		abort();
+	}
 	iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
 	//
-	bins = (uint16_t*)calloc(BAM_MAX_BIN, 2);
+	if ((bins = (uint16_t*)calloc(BAM_MAX_BIN, 2)) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate bin array.\n", __func__);
+		abort();
+	}
 	n_bins = reg2bins(beg, end, bins);
 	index = idx->index[tid];
 	if (idx->index2[tid].n > 0) {
 		min_off = (beg>>BAM_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
 			: idx->index2[tid].offset[beg>>BAM_LIDX_SHIFT];
 		if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
-			int n = beg>>BAM_LIDX_SHIFT;
+			int n = beg >> BAM_LIDX_SHIFT;
 			if (n > idx->index2[tid].n) n = idx->index2[tid].n;
 			for (i = n - 1; i >= 0; --i)
 				if (idx->index2[tid].offset[i] != 0) break;
@@ -717,7 +808,10 @@ bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
 	if (n_off == 0) {
 		free(bins); return iter;
 	}
-	off = (pair64_t*)calloc(n_off, 16);
+	if ((off = (pair64_t*)calloc(n_off, 16)) == NULL) {
+		fprintf(stderr, "[%s] failed to allocate offset pair array.\n", __func__);
+		abort();
+	}
 	for (i = n_off = 0; i < n_bins; ++i) {
 		if ((k = kh_get(i, index, bins[i])) != kh_end(index)) {
 			int j;
@@ -732,6 +826,10 @@ bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
 	}
 	{
 		bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
+		if (b == NULL) {
+			fprintf(stderr, "[%s] failure to allocate bam1_t buffer.\n", __func__);
+			abort();
+		}
 		int l;
 		ks_introsort(off, n_off, off);
 		// resolve completely contained adjacent blocks