static void gt_seqfilter_arguments_delete(void *tool_arguments) { SeqFilterArguments *arguments = tool_arguments; if (!arguments) return; gt_file_delete(arguments->outfp); gt_outputfileinfo_delete(arguments->ofi); gt_free(arguments); }
static void gt_seqmutate_arguments_delete(void *tool_arguments) { MutateArguments *arguments = tool_arguments; if (!arguments) return; gt_file_delete(arguments->outfp); gt_outputfileinfo_delete(arguments->ofi); gt_free(arguments); }
static void gt_mergefeat_arguments_delete(void *tool_arguments) { InterFeatArguments *arguments = tool_arguments; if (!arguments) return; gt_file_delete(arguments->outfp); gt_outputfileinfo_delete(arguments->ofi); gt_free(arguments); }
static void gt_cds_arguments_delete(void *tool_arguments) { CDSArguments *arguments = tool_arguments; if (!arguments) return; gt_file_delete(arguments->outfp); gt_outputfileinfo_delete(arguments->ofi); gt_seqid2file_info_delete(arguments->s2fi); gt_free(arguments); }
static void gt_splicesiteinfo_arguments_delete(void *tool_arguments) { SpliceSiteInfoArguments *arguments = tool_arguments; if (!arguments) return; gt_file_delete(arguments->outfp); gt_outputfileinfo_delete(arguments->ofi); gt_seqid2file_info_delete(arguments->s2fi); gt_free(arguments); }
static void gt_extractseq_arguments_delete(void *tool_arguments) { ExtractSeqArguments *arguments = tool_arguments; if (!arguments) return; gt_file_delete(arguments->outfp); gt_outputfileinfo_delete(arguments->ofi); gt_str_delete(arguments->fastakeyfile); gt_str_delete(arguments->pattern); gt_free(arguments); }
static void gt_ltrdigest_arguments_delete(void *tool_arguments) { GtLTRdigestOptions *arguments = tool_arguments; if (!arguments) return; #ifdef HAVE_HMMER gt_str_array_delete(arguments->pdom_opts.hmm_files); #endif gt_str_delete(arguments->trna_lib); gt_str_delete(arguments->prefix); gt_str_delete(arguments->cutoffs); gt_file_delete(arguments->outfp); gt_outputfileinfo_delete(arguments->ofi); gt_free(arguments); }
static GtOPrval parse_options(int *parsed_args, ChseqidsArguments *arguments, int argc, const char **argv, GtError *err) { GtOptionParser *op; GtOutputFileInfo *ofi; GtOption *option; GtOPrval oprval; gt_error_check(err); /* init */ op = gt_option_parser_new("[option ...] mapping_file [GFF3_file]", "Change sequence ids by the mapping given in " "mapping_file."); ofi = gt_outputfileinfo_new(); /* -sort */ option = gt_option_new_bool("sort", "sort the GFF3 features after changing the " "sequence ids\n(memory consumption is " "proportional to the input file size)", &arguments->sort, false); gt_option_parser_add_option(op, option); /* -v */ option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); /* output file options */ gt_outputfile_register_options(op, &arguments->outfp, ofi); /* parse options */ gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL); gt_option_parser_set_min_max_args(op, 1, 2); oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc, err); /* free */ gt_outputfileinfo_delete(ofi); gt_option_parser_delete(op); return oprval; }