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;
}
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) {
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);
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;
}
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;
{
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;
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);
}
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;
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) {
}
}
// 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);
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"
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
++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);
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;
}
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;
}
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;
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;
}
{
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
projects / samtools.git / blobdiff