static int parse_bed_range(GtRange *range, GtStr *start, GtStr *end,
GtWord offset, GtIO *bed_file, bool thick,
GtError *err)
{
int had_err;
gt_error_check(err);
had_err = gt_parse_range(range, gt_str_get(start), gt_str_get(end),
gt_io_get_line_number(bed_file),
gt_io_get_filename(bed_file), err);
/* BED has a weird numbering scheme: positions are 0-based, but the end
position is not part of the feature. Transform to 1-based coordinates. */
range->start++;
/* Ranges defining a 'thick' region sometimes come with length 0 to
designate that there are no thick regions. So do not fail here and
handle that case later. */
if (!thick) {
if (!had_err && range->start > range->end) {
gt_error_set(err, "file \"%s\": line "GT_WU": BED feature has length 0",
gt_io_get_filename(bed_file),
gt_io_get_line_number(bed_file));
had_err = -1;
}
}
if (offset)
*range = gt_range_offset(range, offset);
return had_err;
}
static int parse_bed_range(GtRange *range, GtStr *start, GtStr *end,
long offset, GtIO *bed_file, GtError *err)
{
int had_err;
gt_error_check(err);
had_err = gt_parse_range(range, gt_str_get(start), gt_str_get(end),
gt_io_get_line_number(bed_file),
gt_io_get_filename(bed_file), err);
/* BED has a weird numbering scheme: positions are 0-based, but the end
position is not part of the feature. Transform to 1-based coordinates. */
range->start++;
if (!had_err && range->start > range->end) {
gt_error_set(err, "file \"%s\": line %lu: BED feature has length 0",
gt_io_get_filename(bed_file), gt_io_get_line_number(bed_file));
had_err = -1;
}
if (offset)
*range = gt_range_offset(range, offset);
return had_err;
}
static void make_sequence_region(GtHashmap *sequence_regions,
GtStr *sequenceid,
GthRegionFactory *srf,
GthInput *input,
GtUword filenum,
GtUword seqnum)
{
GtUword offset_is_defined = false;
GtRange range, descrange;
GtGenomeNode *sr = NULL;
gt_assert(sequence_regions && sequenceid && srf && input);
if (gth_input_use_substring_spec(input)) {
range.start = gth_input_genomic_substring_from(input);
range.end = gth_input_genomic_substring_to(input);
}
else {
range = gth_input_get_relative_genomic_range(input, filenum, seqnum);
}
if (srf->use_desc_ranges) {
GtStr *description = gt_str_new();
gth_input_get_genomic_description(input, description, filenum, seqnum);
if (!gt_parse_description_range(gt_str_get(description), &descrange))
offset_is_defined = true;
gt_str_delete(description);
}
if (offset_is_defined)
range = gt_range_offset(&range, descrange.start);
else
range = gt_range_offset(&range, 1); /* 1-based */
if (!gt_str_length(sequenceid) ||
(gt_cstr_table_get(srf->used_seqids, gt_str_get(sequenceid)) &&
!offset_is_defined)) {
/* sequenceid is empty or exists already (and no offset has been parsed)
-> make one up */
GtStr *seqid;
char *base;
base = gt_basename(gth_input_get_genomic_filename(input, filenum));
seqid = gt_str_new_cstr(base);
gt_free(base);
gt_str_append_char(seqid, '|');
gt_str_append_uword(seqid, seqnum + 1); /* 1-based */
seqid_store_add(srf->seqid_store, filenum, seqnum, seqid, GT_UNDEF_UWORD);
gt_assert(!gt_cstr_table_get(srf->used_seqids, gt_str_get(seqid)));
gt_cstr_table_add(srf->used_seqids, gt_str_get(seqid));
sr = gt_region_node_new(seqid_store_get(srf->seqid_store, filenum, seqnum),
range.start, range.end);
gt_hashmap_add(sequence_regions,
(void*) gt_cstr_table_get(srf->used_seqids,
gt_str_get(seqid)),
sr);
gt_str_delete(seqid);
}
else {
/* sequenceid does not exists already (or an offset has been parsed)
-> use this one */
if (!gt_cstr_table_get(srf->used_seqids, gt_str_get(sequenceid))) {
/* no sequence region with this id exists -> create one */
gt_cstr_table_add(srf->used_seqids, gt_str_get(sequenceid));
seqid_store_add(srf->seqid_store, filenum, seqnum, sequenceid,
offset_is_defined ? descrange.start : GT_UNDEF_UWORD);
sr = gt_region_node_new(seqid_store_get(srf->seqid_store, filenum,
seqnum), range.start, range.end);
gt_hashmap_add(sequence_regions,
(void*) gt_cstr_table_get(srf->used_seqids,
gt_str_get(sequenceid)),
sr);
}
else {
GtRange prev_range, new_range;
/* sequence region with this id exists already -> modify range */
sr = gt_hashmap_get(sequence_regions, gt_str_get(sequenceid));
gt_assert(sr);
prev_range = gt_genome_node_get_range(sr);
new_range = gt_range_join(&prev_range, &range);
gt_genome_node_set_range(sr, &new_range);
seqid_store_add(srf->seqid_store, filenum, seqnum, sequenceid,
offset_is_defined ? descrange.start : GT_UNDEF_UWORD);
}
}
gt_assert(sr);
}
