l->list[l->n].u = beg; l->list[l->n++].v = end;
}
-static inline void insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
+static inline uint64_t insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
{
int i, beg, end;
beg = _beg >> TAD_LIDX_SHIFT;
if (index2->offset[i] == 0) index2->offset[i] = offset;
}
if (index2->n < end + 1) index2->n = end + 1;
+ return (uint64_t)beg<<32 | end;
}
static void merge_chunks(ti_index_t *idx)
ti_index_t *idx;
uint32_t last_bin, save_bin;
int32_t last_coor, last_tid, save_tid;
- uint64_t save_off, last_off, lineno = 0;
+ uint64_t save_off, last_off, lineno = 0, offset0 = (uint64_t)-1, tmp;
kstring_t *str;
str = calloc(1, sizeof(kstring_t));
}
get_intv(idx, str, &intv);
if (last_tid != intv.tid) { // change of chromosomes
+ if (last_tid>intv.tid )
+ {
+ fprintf(stderr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted?\n",(unsigned long long)lineno);
+ exit(1);
+ }
last_tid = intv.tid;
last_bin = 0xffffffffu;
} else if (last_coor > intv.beg) {
fprintf(stderr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno);
exit(1);
}
- insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
+ tmp = insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
+ if (last_off == 0) offset0 = tmp;
if (intv.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 (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
merge_chunks(idx);
fill_missing(idx);
+ if (offset0 != (uint64_t)-1 && idx->n && idx->index2[0].offset) {
+ int i, beg = offset0>>32, end = offset0&0xffffffffu;
+ for (i = beg; i <= end; ++i) idx->index2[0].offset[i] = 0;
+ }
free(str->s); free(str);
return idx;
char *fname = get_local_version(fn);
if (fname == 0) return 0;
idx = ti_index_load_local(fname);
+ if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load the index: %s\n", fname);
free(fname);
- if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load BAM index.\n");
return idx;
}
BGZF *fp, *fpidx;
ti_index_t *idx;
if ((fp = bgzf_open(fn, "r")) == 0) {
- fprintf(stderr, "[ti_index_build2] fail to open the BAM file.\n");
+ fprintf(stderr, "[ti_index_build2] fail to open the file: %s\n", fn);
return -1;
}
idx = ti_index_core(fp, conf);
if (p->list[j].v > min_off) off[n_off++] = p->list[j];
}
}
+ if (n_off == 0) {
+ free(bins); free(off); return iter;
+ }
free(bins);
{
int l;