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;
}
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;
{
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];
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);
}
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));
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) < p->n) {
+ 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) {
}
}
// 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);
+ 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;
+ }
if (bam_is_be)
for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
}
}
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");
+ break;
+ }
free(buf);
fclose(fp);
knet_close(fp_remote);
}
idx = bam_index_core(fp);
bam_close(fp);
+ if(idx == 0) {
+ fprintf(stderr, "[bam_index_build2] fail to index the BAM file.\n");
+ return -1;
+ }
if (_fnidx == 0) {
fnidx = (char*)calloc(strlen(fn) + 5, 1);
strcpy(fnidx, fn); strcat(fnidx, ".bai");
}
}
free(bins);
+ if (n_off == 0) {
+ free(off); return iter;
+ }
{
bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
int l;
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;
}
projects / samtools.git / blobdiff