static int gt_gff3_runner(int argc, const char **argv, int parsed_args, void *tool_arguments, GtError *err) { GFF3Arguments *arguments = tool_arguments; GtTypeChecker *type_checker = NULL; GtNodeStream *gff3_in_stream, *sort_stream = NULL, *load_stream = NULL, *merge_feature_stream = NULL, *add_introns_stream = NULL, *set_source_stream = NULL, *gff3_out_stream = NULL, *last_stream; int had_err = 0; gt_error_check(err); gt_assert(arguments); /* create a gff3 input stream */ gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args, argv + parsed_args); if (arguments->verbose && arguments->outfp) gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream); if (arguments->checkids) gt_gff3_in_stream_check_id_attributes((GtGFF3InStream*) gff3_in_stream); if (!arguments->addids) gt_gff3_in_stream_disable_add_ids(gff3_in_stream); last_stream = gff3_in_stream; /* set different type checker if necessary */ if (gt_typecheck_info_option_used(arguments->tci)) { type_checker = gt_typecheck_info_create_type_checker(arguments->tci, err); if (!type_checker) had_err = -1; if (!had_err) gt_gff3_in_stream_set_type_checker(gff3_in_stream, type_checker); } /* set offset (if necessary) */ if (!had_err && arguments->offset != GT_UNDEF_WORD) gt_gff3_in_stream_set_offset(gff3_in_stream, arguments->offset); /* set offsetfile (if necessary) */ if (!had_err && gt_str_length(arguments->offsetfile)) { had_err = gt_gff3_in_stream_set_offsetfile(gff3_in_stream, arguments->offsetfile, err); } /* enable strict mode (if necessary) */ if (!had_err && arguments->strict) gt_gff3_in_stream_enable_strict_mode((GtGFF3InStream*) gff3_in_stream); /* enable tidy mode (if necessary) */ if (!had_err && arguments->tidy) gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream*) gff3_in_stream); if (!had_err && arguments->fixboundaries) gt_gff3_in_stream_fix_region_boundaries((GtGFF3InStream*) gff3_in_stream); /* create load stream (if necessary) */ if (!had_err && arguments->load) { load_stream = gt_load_stream_new(last_stream); last_stream = load_stream; } /* create sort stream (if necessary) */ if (!had_err && arguments->sort) { sort_stream = gt_sort_stream_new(last_stream); last_stream = sort_stream; } /* create merge feature stream (if necessary) */ if (!had_err && arguments->mergefeat) { gt_assert(sort_stream); merge_feature_stream = gt_merge_feature_stream_new(sort_stream); last_stream = merge_feature_stream; } /* create addintrons stream (if necessary) */ if (!had_err && arguments->addintrons) { gt_assert(last_stream); add_introns_stream = gt_add_introns_stream_new(last_stream); last_stream = add_introns_stream; } /* create setsource stream (if necessary) */ if (!had_err && gt_str_length(arguments->newsource) > 0) { gt_assert(last_stream); GtNodeVisitor *ssv = gt_set_source_visitor_new(arguments->newsource); set_source_stream = gt_visitor_stream_new(last_stream, ssv); last_stream = set_source_stream; } /* create gff3 output stream */ if (!had_err && arguments->show) { gff3_out_stream = gt_gff3_out_stream_new(last_stream, arguments->outfp); last_stream = gff3_out_stream; gt_gff3_out_stream_set_fasta_width((GtGFF3OutStream*) last_stream, arguments->width); if (arguments->retainids) gt_gff3_out_stream_retain_id_attributes((GtGFF3OutStream*) last_stream); } /* pull the features through the stream and free them afterwards */ if (!had_err) had_err = gt_node_stream_pull(last_stream, err); /* free */ gt_node_stream_delete(gff3_out_stream); gt_node_stream_delete(sort_stream); gt_node_stream_delete(load_stream); gt_node_stream_delete(merge_feature_stream); gt_node_stream_delete(add_introns_stream); gt_node_stream_delete(set_source_stream); gt_node_stream_delete(gff3_in_stream); gt_type_checker_delete(type_checker); return had_err; }
// Main method int main(int argc, char * const *argv) { GtError *error; GtLogger *logger; GtQueue *streams; GtNodeStream *stream, *last_stream; CanonGFF3Options options = { NULL, NULL, false }; gt_lib_init(); error = gt_error_new(); canon_gff3_parse_options(argc, argv + 0, &options, error); streams = gt_queue_new(); logger = gt_logger_new(true, "", stderr); stream = gt_gff3_in_stream_new_unsorted(argc - optind, (const char **) argv+optind); gt_gff3_in_stream_check_id_attributes((GtGFF3InStream *)stream); gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream *)stream); gt_queue_add(streams, stream); last_stream = stream; if(options.infer) { GtHashmap *type_parents = gt_hashmap_new(GT_HASH_STRING, gt_free_func, gt_free_func); gt_hashmap_add(type_parents, gt_cstr_dup("mRNA"), gt_cstr_dup("gene")); gt_hashmap_add(type_parents, gt_cstr_dup("tRNA"), gt_cstr_dup("gene")); stream = agn_infer_parent_stream_new(last_stream, type_parents); gt_hashmap_delete(type_parents); gt_queue_add(streams, stream); last_stream = stream; } stream = agn_gene_stream_new(last_stream, logger); gt_queue_add(streams, stream); last_stream = stream; if(options.source != NULL) { GtNodeVisitor *ssv = gt_set_source_visitor_new(options.source); stream = gt_visitor_stream_new(last_stream, ssv); gt_queue_add(streams, stream); last_stream = stream; } stream = gt_gff3_out_stream_new(last_stream, options.outstream); if(!options.infer) gt_gff3_out_stream_retain_id_attributes((GtGFF3OutStream *)stream); gt_queue_add(streams, stream); last_stream = stream; if(gt_node_stream_pull(last_stream, error) == -1) { fprintf(stderr, "[CanonGFF3] error processing node stream: %s", gt_error_get(error)); } while(gt_queue_size(streams) > 0) { stream = gt_queue_get(streams); gt_node_stream_delete(stream); } gt_queue_delete(streams); if(options.source != NULL) gt_str_delete(options.source); if(options.outstream != NULL) gt_file_delete(options.outstream); gt_error_delete(error); gt_logger_delete(logger); gt_lib_clean(); return 0; }