static void* gt_cds_arguments_new(void)
{
CDSArguments *arguments = gt_calloc(1, sizeof *arguments);
arguments->s2fi = gt_seqid2file_info_new();
arguments->ofi = gt_outputfileinfo_new();
return arguments;
}
static void* gt_splicesiteinfo_arguments_new(void)
{
SpliceSiteInfoArguments *arguments = gt_calloc(1, sizeof *arguments);
arguments->s2fi = gt_seqid2file_info_new();
arguments->ofi = gt_outputfileinfo_new();
return arguments;
}
static void* gt_extractseq_arguments_new(void)
{
ExtractSeqArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
arguments->pattern = gt_str_new();
arguments->fastakeyfile = gt_str_new();
arguments->ofi = gt_outputfileinfo_new();
return arguments;
}
static void* gt_ltrdigest_arguments_new(void)
{
GtLTRdigestOptions *arguments = gt_calloc((size_t) 1, sizeof *arguments);
memset(arguments, 0, sizeof *arguments);
#ifdef HAVE_HMMER
arguments->pdom_opts.hmm_files = gt_str_array_new();
#endif
arguments->trna_lib = gt_str_new();
arguments->prefix = gt_str_new();
arguments->cutoffs = gt_str_new();
arguments->ofi = gt_outputfileinfo_new();
return 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;
}
static void* gt_seqmutate_arguments_new(void)
{
MutateArguments *arguments = gt_calloc(1, sizeof *arguments);
arguments->ofi = gt_outputfileinfo_new();
return arguments;
}
static void* gt_seqfilter_arguments_new(void)
{
SeqFilterArguments *arguments = gt_calloc(1, sizeof *arguments);
arguments->ofi = gt_outputfileinfo_new();
return arguments;
}
static void* gt_mergefeat_arguments_new(void)
{
InterFeatArguments *arguments = gt_calloc(1, sizeof *arguments);
arguments->ofi = gt_outputfileinfo_new();
return arguments;
}
static void* gt_seqtransform_arguments_new(void)
{
SeqtransformArguments *arguments = gt_calloc(1, sizeof *arguments);
arguments->ofi = gt_outputfileinfo_new();
return arguments;
}
