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); }
GtStr* gth_region_factory_get_seqid(GthRegionFactory *srf, GtUword filenum, GtUword seqnum) { gt_assert(srf && srf->factory_was_used); return seqid_store_get(srf->seqid_store, filenum, seqnum); }
GtStr* gth_region_factory_get_seqid(GthRegionFactory *srf, unsigned long filenum, unsigned long seqnum) { gt_assert(srf && srf->factory_was_used); return seqid_store_get(srf->seqid_store, filenum, seqnum); }