X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=bam_index.c;h=c7f33959bd99ddef3a9a628d885e450fc2e07acf;hb=a96da304bf130abb0d49b60f80d2b722305545d5;hp=f60a6f874b106f03c655d1207dddf21c4df7fc48;hpb=6a0c6f060a60789b48e10a72b1381f6e54599302;p=samtools.git

diff --git a/bam_index.c b/bam_index.c
index f60a6f8..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) {
@@ -159,32 +168,54 @@ 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;
-    n_mapped = n_unmapped = n_no_coor = off_end = 0;
+	n_mapped = n_unmapped = n_no_coor = off_end = 0;
 	off_beg = off_end = bam_tell(fp);
 	while ((ret = bam_read1(fp, b)) >= 0) {
 		if (c->tid < 0) ++n_no_coor;
-		if (last_tid != c->tid) { // change of chromosomes
+		if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes
 			last_tid = c->tid;
 			last_bin = 0xffffffffu;
-		} else if (last_coor > c->pos) {
+		} else if ((uint32_t)last_tid > (uint32_t)c->tid) {
+			fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr\n",
+					bam1_qname(b), last_tid+1, c->tid+1);
+			return NULL;
+		} else if ((int32_t)c->tid >= 0 && last_coor > c->pos) {
 			fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n",
 					bam1_qname(b), last_coor, c->pos, c->tid+1);
-			exit(1);
+			return NULL;
 		}
-		if (c->tid >= 0) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+		if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) insert_offset2(&idx->index2[b->core.tid], b, last_off);
 		if (c->bin != last_bin) { // then possibly write the binning index
 			if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
 				insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
@@ -203,7 +234,7 @@ bam_index_t *bam_index_core(bamFile fp)
 		if (bam_tell(fp) <= last_off) {
 			fprintf(stderr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n",
 					(unsigned long long)bam_tell(fp), (unsigned long long)last_off);
-			exit(1);
+			return NULL;
 		}
 		if (c->flag & BAM_FUNMAP) ++n_unmapped;
 		else ++n_mapped;
@@ -212,13 +243,20 @@ bam_index_t *bam_index_core(bamFile fp)
 	}
 	if (save_tid >= 0) {
 		insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
-		insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, off_end);
+		insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp));
 		insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
 	}
 	merge_chunks(idx);
 	fill_missing(idx);
-	if (ret >= 0)
-		while ((ret = bam_read1(fp, b)) >= 0) ++n_no_coor;
+	if (ret >= 0) {
+		while ((ret = bam_read1(fp, b)) >= 0) {
+			++n_no_coor;
+			if (c->tid >= 0 && n_no_coor) {
+				fprintf(stderr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
+				return NULL;
+			}
+		}
+	}
 	if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
 	free(b->data); free(b);
 	idx->n_no_coor = n_no_coor;
@@ -248,11 +286,23 @@ 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;
@@ -260,49 +310,100 @@ 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);
 }
@@ -316,17 +417,42 @@ 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 ((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;
@@ -336,18 +462,48 @@ 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__);
+			free(idx->index);
+			free(idx);
+			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__);
+				free(idx->index);
+				free(idx);
+				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__);
+				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);
-			fread(p->list, 16, p->n, fp);
+			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;
+			}
 			if (bam_is_be) {
 				int x;
 				for (x = 0; x < p->n; ++x) {
@@ -357,13 +513,37 @@ 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__);
+			free(idx->index);
+			free(idx);
+			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;
+			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;
+			}
+			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);
@@ -382,7 +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"
@@ -398,7 +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
@@ -417,17 +605,25 @@ 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);
-	while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
-		fwrite(buf, 1, l, fp);
+	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] failed to write to destination file.\n", __func__);
+			break;
+		}
+	}
 	free(buf);
 	fclose(fp);
 	knet_close(fp_remote);
@@ -445,12 +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;
 }
 
@@ -461,18 +661,22 @@ 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, "[%s] fail to index the BAM file.\n", __func__);
+		return -1;
+	}
 	if (_fnidx == 0) {
 		fnidx = (char*)calloc(strlen(fn) + 5, 1);
 		strcpy(fnidx, fn); strcat(fnidx, ".bai");
 	} 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;
 	}
@@ -574,17 +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;
@@ -598,7 +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;
@@ -613,6 +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
@@ -698,6 +915,7 @@ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, voi
 	b = bam_init1();
 	iter = bam_iter_query(idx, tid, beg, end);
 	while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
+	bam_iter_destroy(iter);
 	bam_destroy1(b);
 	return (ret == -1)? 0 : ret;
 }