bam_header_t *h;
int i, ret;
bam_index_t *idx;
- uint32_t last_bin, save_bin;
+ uint32_t last_bin, save_bin, recalculated_bin;
int32_t last_coor, last_tid, save_tid;
bam1_core_t *c;
uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
+ h = bam_header_read(fp);
+ if(h == 0) {
+ fprintf(stderr, "[bam_index_core] Invalid BAM header.");
+ return NULL;
+ }
+
idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
b = (bam1_t*)calloc(1, sizeof(bam1_t));
- 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*));
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));
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_tid > c->tid) {
+ } 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 (last_coor > c->pos) {
+ } 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);
return NULL;
}
- if (c->tid >= 0) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+ if (c->tid >= 0) {
+ if (c->n_cigar) {
+ recalculated_bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
+ } else {
+ recalculated_bin = bam_reg2bin(c->pos, c->pos + 1);
+ }
+ if (c->bin != recalculated_bin) {
+ fprintf(stderr, "[bam_index_core] read '%s' mapped to '%s' at POS %d to %d has BIN %d but should be %d\n",
+ bam1_qname(b), h->target_name[c->tid], c->pos + 1, bam_calend(c, bam1_cigar(b)), c->bin, recalculated_bin);
+ fprintf(stderr, "[bam_index_core] Fix it by using BAM->SAM->BAM to force a recalculation of the BIN field\n");
+ return NULL;
+ }
+ }
+ 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);
last_off = bam_tell(fp);
last_coor = b->core.pos;
}
+ bam_header_destroy(h);
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, bam_tell(fp));
strcat(strcpy(fnidx, fn), ".bai");
fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
download_from_remote(fnidx);
+ free(fnidx);
idx = bam_index_load_local(fn);
}
if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
if (fpidx == 0) {
fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
free(fnidx);
+ bam_index_destroy(idx);
return -1;
}
bam_index_save(idx, fpidx);