static GtOptionParser* gt_seqmutate_option_parser_new(void *tool_arguments)
{
MutateArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *o;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [sequence_file ...]",
"Mutate the sequences of the given sequence "
"file(s).");
/* -rate */
o = gt_option_new_uint_max("rate", "set the mutation rate", &arguments->rate,
1, 100);
gt_option_parser_add_option(op, o);
/* -width */
o = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, o);
gt_outputfile_register_options(op, &arguments->outfp, arguments->ofi);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
return op;
}
static GtIndexOptions* gt_index_options_register_generic_create(
GtOptionParser *op,
GtIndexOptionsIndexType t)
{
GtIndexOptions *idxo;
gt_assert(op != NULL && t != GT_INDEX_OPTIONS_UNDEFINED);
idxo = gt_index_options_new();
idxo->type = t;
idxo->optionprefixlength = gt_option_new_uint_min("pl",
"specify prefix length for bucket sort\n"
"recommendation: use without argument;\n"
"then a reasonable prefix length is "
"automatically determined.",
&idxo->prefixlength,
GT_PREFIXLENGTH_AUTOMATIC,
1U);
gt_option_argument_is_optional(idxo->optionprefixlength);
gt_option_parser_add_option(op, idxo->optionprefixlength);
idxo->optionuserdefinedsortmaxdepth
= gt_option_new_uint_min("sortmaxdepth","sort only up to the given depth.",
&idxo->sfxstrategy.userdefinedsortmaxdepth,
0,
1U);
gt_option_parser_add_option(op, idxo->optionuserdefinedsortmaxdepth);
gt_option_is_development_option(idxo->optionuserdefinedsortmaxdepth);
idxo->optiondifferencecover = gt_option_new_uint_min("dc",
"specify difference cover value",
&idxo->sfxstrategy.differencecover,
0,
4U);
gt_option_parser_add_option(op, idxo->optiondifferencecover);
gt_option_exclude(idxo->optionuserdefinedsortmaxdepth,
idxo->optiondifferencecover);
idxo->optioncmpcharbychar = gt_option_new_bool("cmpcharbychar",
"compare suffixes character "
"by character",
&idxo->sfxstrategy.cmpcharbychar,
false);
gt_option_is_development_option(idxo->optioncmpcharbychar);
gt_option_parser_add_option(op, idxo->optioncmpcharbychar);
idxo->optionnoshortreadsort = gt_option_new_bool("noshortreadsort",
"do not use short read sort",
&idxo->sfxstrategy.noshortreadsort,
false);
gt_option_is_development_option(idxo->optionnoshortreadsort);
gt_option_parser_add_option(op, idxo->optionnoshortreadsort);
idxo->optionmaxwidthrealmedian = gt_option_new_uword("maxwidthrealmedian",
"compute real median for "
"intervals of at most the "
"given widthprefixes",
&idxo->sfxstrategy.
maxwidthrealmedian,
1UL);
gt_option_is_development_option(idxo->optionmaxwidthrealmedian);
gt_option_parser_add_option(op, idxo->optionmaxwidthrealmedian);
idxo->optionalgbounds
= gt_option_new_string_array("algbds",
"length boundaries for the different "
"algorithms to sort buckets of suffixes\n"
"first number: maxbound for insertion sort\n"
"second number: maxbound for blindtrie sort\n"
"third number: maxbound for counting sort",
idxo->algbounds);
gt_option_is_development_option(idxo->optionalgbounds);
gt_option_parser_add_option(op, idxo->optionalgbounds);
idxo->optionstorespecialcodes
= gt_option_new_bool("storespecialcodes",
"store special codes (this may speed up the program)",
&idxo->sfxstrategy.storespecialcodes,false);
gt_option_is_development_option(idxo->optionstorespecialcodes);
gt_option_parser_add_option(op, idxo->optionstorespecialcodes);
idxo->optionparts
= gt_option_new_uint_max("parts",
"specify number of parts in which the index "
"construction is performed",
&idxo->numofparts, 1U, (unsigned) ((1 << 22) - 1));
gt_option_is_development_option(idxo->optionparts);
gt_option_parser_add_option(op, idxo->optionparts);
if (idxo->type == GT_INDEX_OPTIONS_ESA)
{
idxo->optionspmopt = gt_option_new_uint_min("spmopt",
"optimize esa-construction for "
"suffix-prefix matching",
&idxo->sfxstrategy.spmopt_minlength,
0,1U);
gt_option_parser_add_option(op, idxo->optionspmopt);
gt_option_exclude(idxo->optionspmopt, idxo->optiondifferencecover);
idxo->optionmemlimit = gt_option_new_string("memlimit",
"specify maximal amount of memory to be used during "
"index construction (in bytes, the keywords 'MB' "
"and 'GB' are allowed)",
idxo->memlimit, NULL);
gt_option_parser_add_option(op, idxo->optionmemlimit);
gt_option_exclude(idxo->optionmemlimit, idxo->optionparts);
}
idxo->option = gt_option_new_bool("iterscan",
"use iteratorbased-kmer scanning",
&idxo->sfxstrategy.iteratorbasedkmerscanning,
false);
gt_option_is_development_option(idxo->option);
gt_option_parser_add_option(op, idxo->option);
idxo->option = gt_option_new_bool("samplewithprefixlengthnull",
"sort sample with prefixlength=0",
&idxo->sfxstrategy.samplewithprefixlengthnull,
false);
gt_option_is_development_option(idxo->option);
gt_option_parser_add_option(op, idxo->option);
idxo->option = gt_option_new_bool("suftabuint",
"use uint32_t for suftab",
&idxo->sfxstrategy.suftabuint,
false);
gt_option_is_development_option(idxo->option);
gt_option_parser_add_option(op, idxo->option);
idxo->option = gt_option_new_bool("onlybucketinsertion",
"perform only bucket insertion",
&idxo->sfxstrategy.onlybucketinsertion,
false);
gt_option_is_development_option(idxo->option);
gt_option_parser_add_option(op, idxo->option);
idxo->option = gt_option_new_bool("kmerswithencseqreader",
"always perform kmerscanning with encseq-reader",
&idxo->sfxstrategy.kmerswithencseqreader,
false);
gt_option_is_development_option(idxo->option);
gt_option_parser_add_option(op, idxo->option);
idxo->option = gt_option_new_bool("dccheck",
"check intermediate results in difference cover",
&idxo->sfxstrategy.dccheck,
false);
gt_option_is_development_option(idxo->option);
gt_option_parser_add_option(op, idxo->option);
idxo->option = gt_option_new_bool("withradixsort",
"use radixsort to sort the buckets",
&idxo->sfxstrategy.withradixsort,
false);
gt_option_is_development_option(idxo->option);
gt_option_parser_add_option(op, idxo->option);
idxo->option = gt_option_new_bool("compressedoutput",
"output suftab and lcptab in compressed "
"form",
&idxo->sfxstrategy.compressedoutput,
false);
gt_option_is_development_option(idxo->option);
gt_option_parser_add_option(op, idxo->option);
gt_option_parser_register_hook(op, gt_index_options_check_set_create_opts,
idxo);
return idxo;
}
static GtOPrval gthsplit_parse_options(int *parsed_args,
Gthsplitinfo *gthsplitinfo,
int argc, const char **argv,
const GthPlugins *plugins, GtError *err)
{
GtOptionParser *op;
GtOption *optalignmentscore, *optcoverage, *optrange, *optverbose, *optgzip,
*optbzip2, *optforce;
bool alignmentscore, coverage, verbose, gzip, bzip2;
GtOPrval oprval;
gt_error_check(err);
op = gt_option_parser_new("-alignmentscore | -coverage [option ...] "
"[file ...]", "Split GenomeThreader output files "
"containing intermediate results.");
/* specify all options with a corresponding help-text */
optalignmentscore = gt_option_new_bool("alignmentscore", "split according to "
"the overall alignment score (scr)",
&alignmentscore, false);
gt_option_parser_add_option(op, optalignmentscore);
optcoverage = gt_option_new_bool("coverage", "split according to coverage "
"(cov)", &coverage, false);
gt_option_parser_add_option(op, optcoverage);
optrange = gt_option_new_uint_max(RANGE_OPT_CSTR, "set the percentage range "
"used to create the sets",
>hsplitinfo->range, DEFAULT_RANGE, 100);
gt_option_parser_add_option(op, optrange);
/* add sa_filter options */
gth_sa_filter_register_options(op, gthsplitinfo->sa_filter, false);
/* -v */
optverbose = gt_option_new_verbose(&verbose);
gt_option_parser_add_option(op, optverbose);
optgzip = gt_option_new_bool("gzip", "write gzip compressed output file(s)",
&gzip, false);
gt_option_parser_add_option(op, optgzip);
optbzip2 = gt_option_new_bool("bzip2", "write bzip2 compressed output "
"file(s)", &bzip2, false);
gt_option_parser_add_option(op, optbzip2);
optforce = gt_option_new_bool(GT_FORCE_OPT_CSTR,"force writing to split "
"files", >hsplitinfo->force, false);
gt_option_parser_add_option(op, optforce);
gt_option_exclude(optalignmentscore, optcoverage);
gt_option_exclude(optgzip, optbzip2);
gt_option_is_mandatory_either(optalignmentscore, optcoverage);
gt_option_parser_set_mail_address(op, "<*****@*****.**>");
oprval = gt_option_parser_parse(op, parsed_args, argc, argv,
plugins->gth_version_func, err);
if (oprval == GT_OPTION_PARSER_OK && alignmentscore)
gthsplitinfo->splitmode = ALIGNMENTSCORE_SPLIT;
if (oprval == GT_OPTION_PARSER_OK && coverage)
gthsplitinfo->splitmode = COVERAGE_SPLIT;
if (oprval == GT_OPTION_PARSER_OK && 100 % gthsplitinfo->range) {
gt_error_set(err, "argument to option %s must divide 100 without rest",
RANGE_OPT_CSTR);
oprval = GT_OPTION_PARSER_ERROR;
}
if (oprval == GT_OPTION_PARSER_OK && verbose)
gthsplitinfo->showverbose = gth_show_on_stdout;
if (oprval == GT_OPTION_PARSER_OK && gzip)
gthsplitinfo->file_mode = GT_FILE_MODE_GZIP;
if (oprval == GT_OPTION_PARSER_OK && bzip2)
gthsplitinfo->file_mode = GT_FILE_MODE_BZIP2;
/* save consensus files */
if (oprval == GT_OPTION_PARSER_OK) {
while (*parsed_args < argc) {
gt_str_array_add_cstr(gthsplitinfo->consensusfiles, argv[*parsed_args]);
(*parsed_args)++;
}
}
if (oprval == GT_OPTION_PARSER_OK &&
!gt_str_array_size(gthsplitinfo->consensusfiles) &&
(gt_option_is_set(optgzip) || gt_option_is_set(optbzip2))) {
gt_error_set(err, "to use compression, at least on input file has to be "
"supplied");
oprval = GT_OPTION_PARSER_ERROR;
}
gt_option_parser_delete(op);
return oprval;
}
