GtRegionMapping* gt_region_mapping_new_encseq_seqno(GtEncseq *encseq)
{
GtRegionMapping *rm;
rm = gt_region_mapping_new_encseq(encseq, false, false);
rm->useseqno = true;
return rm;
}
static int gt_tir_runner(GT_UNUSED int argc, GT_UNUSED const char **argv,
GT_UNUSED int parsed_args, void *tool_arguments,
GtError *err)
{
GtTirArguments *arguments = tool_arguments;
GtNodeStream *tir_stream = NULL,
*pdom_stream = NULL,
*gff3_out_stream = NULL,
*last_stream = NULL;
GtPdomModelSet *ms = NULL;
GtRegionMapping *rmap = NULL;
int had_err = 0;
gt_error_check(err);
gt_assert(arguments);
tir_stream = gt_tir_stream_new(arguments->str_indexname,
arguments->min_seed_length,
arguments->min_TIR_length,
arguments->max_TIR_length,
arguments->min_TIR_distance,
arguments->max_TIR_distance,
arguments->arbit_scores,
arguments->xdrop_belowscore,
arguments->similarity_threshold,
arguments->best_overlaps,
arguments->no_overlaps,
arguments->min_TSD_length,
arguments->max_TSD_length,
arguments->vicinity,
err);
if (tir_stream == NULL)
return -1;
last_stream = tir_stream;
rmap = gt_region_mapping_new_encseq((GtEncseq*)
gt_tir_stream_get_encseq((GtTIRStream*) tir_stream),
true, false);
gt_assert(rmap);
if (!had_err && gt_str_array_size(arguments->hmm_files) > 0)
{
if (!strcmp(gt_str_get(arguments->cutoffs), "GA")) {
arguments->cutoff = GT_PHMM_CUTOFF_GA;
} else if (!strcmp(gt_str_get(arguments->cutoffs), "TC")) {
arguments->cutoff = GT_PHMM_CUTOFF_TC;
} else if (!strcmp(gt_str_get(arguments->cutoffs), "NONE")) {
arguments->cutoff = GT_PHMM_CUTOFF_NONE;
} else {
gt_error_set(err, "invalid cutoff setting!");
had_err = -1;
}
}
if (!had_err && gt_str_array_size(arguments->hmm_files) > 0) {
GtNodeVisitor *pdom_v;
ms = gt_pdom_model_set_new(arguments->hmm_files, err);
if (ms != NULL) {
pdom_v = gt_ltrdigest_pdom_visitor_new(ms, arguments->cutoff,
arguments->chain_max_gap_length,
arguments->evalue_cutoff, rmap,
err);
if (pdom_v == NULL)
had_err = -1;
if (!had_err) {
last_stream = pdom_stream = gt_visitor_stream_new(last_stream, pdom_v);
gt_ltrdigest_pdom_visitor_set_root_type((GtLTRdigestPdomVisitor*)
pdom_v,
gt_ft_terminal_inverted_repeat_element);
gt_ltrdigest_pdom_visitor_set_source_tag((GtLTRdigestPdomVisitor*)
pdom_v,
"TIRvish");
}
} else had_err = -1;
}
gff3_out_stream = gt_gff3_out_stream_new(last_stream, NULL);
last_stream = gff3_out_stream;
/* pull the features through the stream and free them afterwards */
if (!had_err)
had_err = gt_node_stream_pull(last_stream, err);
gt_node_stream_delete(tir_stream);
gt_node_stream_delete(pdom_stream);
gt_node_stream_delete(gff3_out_stream);
gt_region_mapping_delete(rmap);
gt_pdom_model_set_delete(ms);
return had_err;
}