static GtOPrval parse_options(GtStr *indexname,GtStrArray *indexnametab,
int *parsed_args, int argc,
const char **argv, GtError *err)
{
GtOptionParser *op;
GtOPrval oprval;
GtOption *option;
gt_error_check(err);
op = gt_option_parser_new("storeindex <mkvindex1> <mkvindex2> ...",
"Merge indexes into one index.");
gt_option_parser_set_mail_address(op,"<*****@*****.**>");
option = gt_option_new_filename_array("ii",
"specify input index files (mandatory)",
indexnametab);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
option = gt_option_new_string("indexname",
"specify index to be created",
indexname, NULL);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
err);
gt_option_parser_delete(op);
return oprval;
}
static GtOptionParser* gt_csa_option_parser_new(void *tool_arguments)
{
CSAArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] [GFF3_file]",
"Transform spliced alignments from GFF3 file into "
"consensus spliced alignments.");
/* -join-length */
option = gt_option_new_uword("join-length", "set join length for the spliced "
"alignment clustering", &arguments->join_length,
GT_DEFAULT_JOIN_LENGTH);
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_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
gt_option_parser_set_max_args(op, 1);
return op;
}
static GtOptionParser* gt_seqtransform_option_parser_new(void *tool_arguments)
{
SeqtransformArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *o;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [sequence_file ...]",
"Perform simple transformations on the given "
"sequence file(s).");
/* -addstopaminos */
o = gt_option_new_bool("addstopaminos", "append stop amino acids ('"
GT_STOP_AMINO_CSTR"') to given protein sequences, if "
"not already present", &arguments->addstopaminos,
false);
gt_option_parser_add_option(op, o);
/* -width */
o = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, o);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
return op;
}
static GtOptionParser* gt_encseq_check_option_parser_new(void *tool_arguments)
{
GtEncseqCheckArguments *arguments = tool_arguments;
GtOptionParser *op;
GT_UNUSED GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] [file]",
"Check the consistency of an encoded "
"sequence file.");
option = gt_option_new_ulong("scantrials", "specify number of scan trials",
&arguments->scantrials, 0);
gt_option_parser_add_option(op, option);
option = gt_option_new_ulong("multicharcmptrials",
"specify number of multicharacter trials",
&arguments->multicharcmptrials, 0);
gt_option_parser_add_option(op, option);
option = gt_option_new_ulong_min_max("prefixlength",
"prefix length",
&arguments->prefixlength, 0,
0, MAXPREFIXLENGTH);
gt_option_parser_add_option(op, option);
gt_option_parser_set_min_args(op, 1);
return op;
}
static GtOptionParser* gt_shredder_option_parser_new(void *tool_arguments)
{
GtShredderArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *o;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [sequence_file ...]",
"GtShredder sequence_file into consecutive pieces of "
"random length.");
o = gt_option_new_ulong_min("coverage", "set the number of times the "
"sequence_file is shreddered", &arguments->coverage,
1, 1);
gt_option_parser_add_option(op, o);
o = gt_option_new_ulong("minlength",
"set the minimum length of the shreddered "
"fragments", &arguments->minlength, 300);
gt_option_parser_add_option(op, o);
o = gt_option_new_ulong("maxlength",
"set the maximum length of the shreddered "
"fragments", &arguments->maxlength, 700);
gt_option_parser_add_option(op, o);
o = gt_option_new_ulong("overlap", "set the overlap between consecutive "
"pieces", &arguments->overlap, 0);
gt_option_parser_add_option(op, o);
o = gt_option_new_probability("sample", "take samples of the generated "
"sequences pieces with the given probability",
&arguments->sample_probability, 1.0);
gt_option_parser_add_option(op, o);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
return op;
}
static GtOptionParser* gt_seqtranslate_option_parser_new(void *tool_arguments)
{
GtTranslateArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] [files]",
"Translates a nucleotide sequence into a protein "
"sequence.");
option = gt_option_new_bool("reverse", "also translate reverse complements",
&arguments->reverse, true);
gt_option_parser_add_option(op, option);
option = gt_option_new_uword("fastawidth", "width of the FASTA output",
&arguments->fasta_width, 60);
gt_option_parser_add_option(op, option);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
gt_option_parser_set_min_args(op, 1);
return op;
}
static GtOptionParser* gt_interfeat_option_parser_new(void *tool_arguments)
{
InterFeatArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Duplicate "
"internal feature nodes in given GFF3 files.");
/* -outside */
option = gt_option_new_string("dest", "set destination type",
arguments->dest_type, NULL);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
/* -inter */
option = gt_option_new_string("source", "set source type",
arguments->source_type, NULL);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
/* output file options */
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
return op;
}
static GtOptionParser* gt_gff3validator_option_parser_new(void *tool_arguments)
{
GFF3ValidatorArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] [GFF3_file ...]",
"Strictly validate given GFF3 files.");
/* typecheck options */
gt_typecheck_info_register_options(arguments->tci, op);
/* xrfcheck options */
gt_xrfcheck_info_register_options(arguments->xci, op);
/* -strict */
option = gt_option_new_bool("strict", "be very strict during GFF3 parsing "
"(stricter than the specification requires)",
&arguments->strict, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
return op;
}
static GtOptionParser* gt_extractfeat_option_parser_new(void *tool_arguments)
{
GtExtractFeatArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [GFF3_file]",
"Extract features given in GFF3 file from "
"sequence file.");
/* -type */
option = gt_option_new_string("type", "set type of features to extract",
arguments->type, NULL);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
/* -join */
option = gt_option_new_bool("join", "join feature sequences in the same "
"subgraph into a single one", &arguments->join,
false);
gt_option_parser_add_option(op, option);
/* -translate */
option = gt_option_new_bool("translate", "translate the features (of a DNA "
"sequence) into protein", &arguments->translate,
false);
gt_option_parser_add_option(op, option);
/* -seqid */
option = gt_option_new_bool("seqid", "add sequence ID of extracted features "
"to FASTA descriptions", &arguments->seqid,
false);
gt_option_parser_add_option(op, option);
/* -target */
option = gt_option_new_bool("target", "add target ID(s) of extracted "
"features to FASTA descriptions",
&arguments->target, false);
gt_option_parser_add_option(op, option);
/* -seqfile, -matchdesc, -usedesc and -regionmapping */
gt_seqid2file_register_options(op, arguments->s2fi);
/* -v */
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
/* -width */
option = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, option);
/* output file options */
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
gt_option_parser_set_max_args(op, 1);
return op;
}
static GtOptionParser* gt_inlineseq_split_option_parser_new(
void *tool_arguments)
{
GtInlineseqSplitArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption GT_UNUSED *option, *seqopt, *gff3opt;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("(-seqfile <seqfile> | -gff3file <gff3file>) "
"[GFF3_file]",
"Split GFF3 annotations with inline sequences into "
"separate files.");
/* -seqfile */
seqopt = gt_option_new_string("seqfile", "output file for sequences as FASTA",
arguments->seqoutfile, NULL);
gt_option_parser_add_option(op, seqopt);
/* -gff3file */
gff3opt = gt_option_new_string("gff3file", "output file for annotations "
"as GFF3",
arguments->gffoutfile, NULL);
gt_option_parser_add_option(op, gff3opt);
gt_option_is_mandatory_either(seqopt, gff3opt);
return op;
}
static GtOptionParser* gt_encseq_bitextract_option_parser_new(void
*tool_arguments)
{
GtEncseqBitextractArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [indexname]",
"Extracts internal data from encoded sequences.");
option = gt_option_new_bool("mirrored", "mirror sequence",
&arguments->mirror, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_ulong("stoppos", "output stop positions",
&arguments->stoppos, GT_UNDEF_ULONG);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("specialranges", "output special ranges",
&arguments->specialranges, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_ulong("bitpos", "extract and display "
"two bit encoding for position",
&arguments->bitpos, GT_UNDEF_ULONG);
gt_option_parser_add_option(op, option);
gt_encseq_options_add_readmode_option(op, arguments->readmode);
gt_option_parser_set_min_args(op, 1U);
return op;
}
static OPrval parse_options(int *parsed_args, RegionCovArguments *arguments,
int argc, const char **argv, GtError *err)
{
GtOptionParser *op;
GtOption *o;
OPrval oprval;
gt_error_check(err);
op = gt_option_parser_new("[option ...] GFF3_file",
"Show which parts of the given sequence regions are "
"covered by features.");
/* -maxfeaturedist */
o = gt_option_new_ulong("maxfeaturedist", "set the maximum distance two "
"features can have while still being in the same "
"``cluster''", &arguments->max_feature_dist, 0);
gt_option_parser_add_option(op, o);
/* -v */
o = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, o);
/* parse */
gt_option_parser_set_min_max_args(op, 1, 1);
oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
err);
gt_option_parser_delete(op);
return oprval;
}
static GtOptionParser* gt_script_filter_option_parser_new(void *tool_arguments)
{
GtScriptFilterArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] [script file(s)]",
"Get info about and validate Lua script filters.");
/* -showinfo */
option = gt_option_new_bool("showinfo", "show information about filter",
&arguments->showinfo, true);
gt_option_parser_add_option(op, option);
/* -validate */
option = gt_option_new_bool("validate", "validate filter function",
&arguments->validate, true);
gt_option_parser_add_option(op, option);
/* -oneline */
option = gt_option_new_bool("oneline", "show compact information on one line",
&arguments->oneline, false);
gt_option_parser_add_option(op, option);
/* -scriptname */
option = gt_option_new_bool("scriptname", "show script name",
&arguments->scriptname, true);
gt_option_parser_add_option(op, option);
gt_option_parser_set_min_args(op, 1);
return op;
}
static GtOptionParser* gt_splicesiteinfo_option_parser_new(void *tool_arguments)
{
SpliceSiteInfoArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Show information "
"about splice sites given in GFF3 files.");
/* -seqfile, -matchdesc, -usedesc and -regionmapping */
gt_seqid2file_register_options(op, arguments->s2fi);
/* -addintrons */
option = gt_option_new_bool("addintrons", "add intron features between "
"existing exon features\n(before computing the "
"information to be shown)",
&arguments->addintrons, false);
gt_option_parser_add_option(op, option);
/* output file options */
gt_outputfile_register_options(op, &arguments->outfp, arguments->ofi);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
return op;
}
static GtOptionParser* gt_compressedbits_option_parser_new(void *tool_arguments)
{
GtCompressdbitsArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...]",
"Testing compressed bitsequence, save to disk, reload.");
/* -size */
option = gt_option_new_ulong("size",
"size of GtBitsequence to create "
"(words 32/64 bit)",
&arguments->size, 20UL);
gt_option_parser_add_option(op, option);
arguments->size_op = gt_option_ref(option);
/* -samplerate */
option = gt_option_new_uint("samplerate",
"samplerate of random GtBitsequence to test",
&arguments->samplerate, 32U);
gt_option_parser_add_option(op, option);
/* -rand */
option = gt_option_new_bool("rand", "create random bitvector",
&arguments->fill_random, false);
gt_option_parser_add_option(op, option);
arguments->rand_op = gt_option_ref(option);
/* -check */
option = gt_option_new_bool("check", "compare original with compressed and "
"loaded from file",
&arguments->check_consistency, false);
gt_option_parser_add_option(op, option);
arguments->rand_op = gt_option_ref(option);
/* -input */
option = gt_option_new_filename(
"input",
"load vector from file, format is as follows:\n"
"[ULL size in bits][[ULL bits]...]\n"
" not usable with -size and -rand",
arguments->filename);
gt_option_parser_add_option(op, option);
arguments->filename_op = gt_option_ref(option);
gt_option_exclude(arguments->filename_op, arguments->size_op);
gt_option_exclude(arguments->filename_op, arguments->rand_op);
/* -benches */
option = gt_option_new_ulong("benches",
"number of function calls to benchmark",
&arguments->benches, 100000UL);
gt_option_parser_add_option(op, option);
return op;
}
static GtOptionParser* gt_seqids_option_parser_new(GT_UNUSED
void *tool_arguments)
{
GtOptionParser *op;
op = gt_option_parser_new("[GFF3_file]",
"Show sequence IDs from annotation file.");
gt_option_parser_set_min_max_args(op, 1, 1);
return op;
}
static GtOptionParser* gt_gff3_to_gtf_option_parser_new(void *tool_arguments)
{
GFF3ToGTFArguments *arguments = tool_arguments;
GtOptionParser *op;
op = gt_option_parser_new("[GFF3_file ...]",
"Parse GFF3 file(s) and show them as GTF2.2.");
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
return op;
}
static GtOptionParser* gt_seqfilter_option_parser_new(void *tool_arguments)
{
SeqFilterArguments *arguments = tool_arguments;
GtOption *option;
GtOptionParser *op;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [sequence_file ...]",
"Filter the given sequence file(s) and show the "
"results on stdout.");
/* -minlength */
option = gt_option_new_uword("minlength",
"set minimum length a sequence must "
"have to pass the filter", &arguments->minlength,
GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option);
/* -maxlength */
option = gt_option_new_uword("maxlength", "set maximum length a sequence can "
"have to pass the filter", &arguments->maxlength,
GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option);
/* -maxseqnum */
option = gt_option_new_uword("maxseqnum", "set the maximum number of "
"sequences which can pass the filter",
&arguments->maxseqnum, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option);
/* -sample */
option = gt_option_new_double_min_max("sample", "set a probability for each "
"sequence to pass the filter",
&arguments->sample_prob,
SEQFILTER_DEF_PROB,
SEQFILTER_MIN_PROB,
SEQFILTER_MAX_PROB);
gt_option_parser_add_option(op, option);
/* -step */
option = gt_option_new_uword_min("step", "only every 'step'-th sequence "
"passes the filter",
&arguments->step,
SEQFILTER_DEF_STEP,
SEQFILTER_MIN_STEP);
gt_option_parser_add_option(op, option);
/* -width */
option = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, option);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
return op;
}
static GtOptionParser*
gt_compreads_compress_option_parser_new(void *tool_arguments)
{
GtCsrHcrEncodeArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
static const char *methods[] = { "page", "regular", "none" };
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] (-files file [...])",
"Generates compact encoding for fastq data.");
option = gt_option_new_bool("descs","encode descriptions",
&arguments->descs, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_filename_array("files", "File(s) containing reads.",
arguments->files);
gt_option_parser_add_option(op, option);
option = gt_option_new_string("name", "specify base name for HCR to be"
" generated. Only mandatory, if more than one"
" file was given.", arguments->name, NULL);
gt_option_parser_add_option(op, option);
option = gt_option_new_string("smap", "file containing alphabet description."
" If \"-smap\" is not set, dna alphabet is"
" used.",
arguments->smap, NULL);
gt_option_parser_add_option(op, option);
option = gt_option_new_range("qrange", "specify range of quality values."
" All values smaller or equal to the lower bound"
" will be converted to the lower bound. All"
" values equal or larger than the upper bound"
" will be converted to the upper bound.",
&arguments->arg_range, NULL);
gt_option_parser_add_option(op, option);
option = gt_option_new_uword("srate", "sampling rate, set to sensible default"
" depending on sampling method",
&arguments->srate, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option);
option = gt_option_new_choice("stype", "type of sampling\n"
"one of regular - page - none",
arguments->method, "page",
methods);
gt_option_parser_add_option(op, option);
gt_option_parser_set_min_max_args(op, 0U, 0U);
return op;
}
static GtOptionParser*
gt_compreads_decompress_option_parser_new(void *tool_arguments)
{
GtCsrHcrDecodeArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] (-file file)",
"Decodes a file of compressed reads.");
option = gt_option_new_bool("v", "be verbose",
&arguments->verbose, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("descs","enable description decoding",
&arguments->descs, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_string("file", "specify base name of files containing"
" HCR.",
arguments->file, NULL);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
option = gt_option_new_string("name", "specify base name for decoded hcr"
" (suffix will be \".fastq\")",
arguments->name, NULL);
gt_option_parser_add_option(op, option);
option = gt_option_new_string("smap", "specify file containing alphabet"
"description (file must be an .al1 file)."
" If \"-smap\" is not set, dna alphabet is"
" used.",
arguments->smap, NULL);
gt_option_parser_add_option(op, option);
option = gt_option_new_range("range", "decode multiple consecutive reads."
" If range is not specified, the "
" entire file will be decoded.",
&arguments->rng, NULL);
gt_option_parser_add_option(op, option);
option = gt_option_new_ulong("benchmark", "decode given number random reads "
"and report the time to do this",
&arguments->bench, 0);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
gt_option_parser_set_min_max_args(op, 0U, 0U);
return op;
}
static GtOptionParser* gt_dev_option_parser_new(void *tool_arguments)
{
GtToolbox *dev_toolbox = tool_arguments;
GtOptionParser *op;
gt_assert(dev_toolbox);
op = gt_option_parser_new("[option ...] dev_tool_name [argument ...]",
"Call development tool with name dev_tool_name and "
"pass argument(s) to it.");
gt_option_parser_set_comment_func(op, gt_toolbox_show, dev_toolbox);
gt_option_parser_set_min_args(op, 1);
return op;
}
static GtOptionParser* gt_packedindex_option_parser_new(void *tool_arguments)
{
GtToolbox *index_toolbox = tool_arguments;
GtOptionParser *op;
gt_assert(index_toolbox);
op = gt_option_parser_new("[option ...] index_tool [argument ...]",
"Call apacked index subtool and pass argument(s) to "
"it.");
gt_option_parser_set_comment_func(op, gt_toolbox_show, index_toolbox);
gt_option_parser_set_min_args(op, 1);
gt_option_parser_refer_to_manual(op);
return op;
}
static GtOptionParser* gt_cds_option_parser_new(void *tool_arguments)
{
CDSArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [GFF3_file]",
"Add CDS (coding sequence) features to exon "
"features given in GFF3 file.");
/* -minorflen */
option = gt_option_new_uint_min("minorflen", "set the minimum length an open "
"reading frame (ORF) must have to be added "
"as a CDS feature (measured in amino acids)",
&arguments->minorflen, 64, 1);
gt_option_parser_add_option(op, option);
/* -startcodon */
option = gt_option_new_bool("startcodon", "require than an ORF must begin "
"with a start codon", &arguments->start_codon,
false);
gt_option_parser_add_option(op, option);
/* -finalstopcodon */
option = gt_option_new_bool("finalstopcodon", "require that the final ORF "
"must end with a stop codon",
&arguments->final_stop_codon, false);
gt_option_parser_add_option(op, option);
/* -genericstartcodons */
option = gt_option_new_bool("genericstartcodons", "use generic start codons",
&arguments->generic_start_codons, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -seqfile, -matchdesc, -usedesc and -regionmapping */
gt_seqid2file_register_options(op, arguments->s2fi);
/* -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, arguments->ofi);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
gt_option_parser_set_max_args(op, 1);
return op;
}
static GtOptionParser* gt_cge_option_parser_new(void *tool_arguments)
{
GtToolbox *index_toolbox = tool_arguments;
GtOptionParser *op;
gt_assert(index_toolbox != NULL);
op = gt_option_parser_new(
"[option ...] congruence_tool [argument ...]",
"Call a congruence subtool and pass argument(s) to it.");
gt_option_parser_set_comment_func(op, gt_toolbox_show, index_toolbox);
gt_option_parser_set_min_args(op, 1U);
gt_option_parser_refer_to_manual(op);
return op;
}
static GtOptionParser* gt_speck_option_parser_new(void *tool_arguments)
{
GtOptionParser *op;
GtOption *option;
SpeccheckArguments *arguments = tool_arguments;
/* init */
op = gt_option_parser_new("[options] [GFF3_file ...]",
"Checks spec definition compliance in GFF3 input.");
option = gt_option_new_filename("specfile",
"file with specification definition",
arguments->specfile);
gt_option_parser_add_option(op, option);
gt_option_is_mandatory(option);
option = gt_option_new_bool("colored", "show colored output",
&arguments->colored, true);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("provideindex", "provide feature index in "
"specfile namespace (requires O(n) memory for n "
"input features)",
&arguments->provideindex, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("sort", "sort input before checking (requires "
"O(n) memory for n input features)",
&arguments->sort, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("failhard", "stop processing and report runtime "
"errors instead of recording them in the results",
&arguments->fail_hard, false);
gt_option_parser_add_option(op, option);
/* -format */
option = gt_option_new_string("output", "output format\n"
"choose from: json, text, html, statsonly",
arguments->format, "text");
gt_option_parser_add_option(op, option);
gt_typecheck_info_register_options_with_default(arguments->tci, op, "so");
gt_seqid2file_register_options_ext(op, arguments->s2fi, false, false);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
return op;
}
static GtOptionParser* gt_sequniq_option_parser_new(void *tool_arguments)
{
GtSequniqArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *seqit_option, *verbose_option, *width_option, *rev_option,
*nofseqs_option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] sequence_file [...] ",
"Filter out repeated sequences in given "
"sequence files.");
/* -seqit */
seqit_option = gt_option_new_bool("seqit", "use sequence iterator",
&arguments->seqit, false);
gt_option_is_development_option(seqit_option);
gt_option_parser_add_option(op, seqit_option);
/* -nofseqs */
nofseqs_option = gt_option_new_uword("nofseqs", "number of sequences "
"(improves efficiency)\ndefault: unspecified",
&arguments->nofseqs, 0);
gt_option_is_development_option(nofseqs_option);
gt_option_hide_default(nofseqs_option);
gt_option_parser_add_option(op, nofseqs_option);
/* -rev */
rev_option = gt_option_new_bool("rev", "also filter out sequences whose "
"reverse complement is identical to a sequence already output",
&arguments->rev, false);
gt_option_parser_add_option(op, rev_option);
/* -v */
verbose_option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, verbose_option);
/* -width */
width_option = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, width_option);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
/* option implications */
gt_option_imply(verbose_option, seqit_option);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
gt_option_parser_set_min_args(op, 1U);
return op;
}
static GtOptionParser*
gt_condenseq_hmmsearch_option_parser_new(void *tool_arguments)
{
GtCondenseqHmmsearchArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] -db DATABASE -hmm HMMPROFILE",
"Perform a hmmsearch on the given compressed "
"database.");
/* -db and -verbose */
gt_condenseq_search_register_options(arguments->csa, op);
/* -hmm */
option = gt_option_new_string("hmm", "hmm query", arguments->hmm, NULL);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
/* -hmmsearch */
option = gt_option_new_string("hmmsearch", "path to hmmsearch, please set if "
"not installed at (linux) default location",
arguments->hmmsearch_path,
"/usr/bin/hmmsearch");
gt_option_parser_add_option(op, option);
/* -tblout */
option = gt_option_new_string("tblout", "file basename to output tabular "
"hmmsearch output to (like hmmer option "
"--tblout). Depending on -max_queries will "
"produce multiple numbered files.",
arguments->outtable_filename, NULL);
gt_option_parser_add_option(op, option);
/* -force_ow */
option = gt_option_new_bool("force_ow", "force overwrite of existing files",
&arguments->force_ow, false);
gt_option_parser_add_option(op, option);
/* -max_queries */
option = gt_option_new_uint("max_queries", "maximum number of queries per "
"fine search, influences file-size and therefore "
"speed!, 0 disables splitting",
&arguments->max_queries, 5U);
gt_option_parser_add_option(op, option);
return op;
}
static GtOptionParser* gt_speck_option_parser_new(void *tool_arguments)
{
GtOptionParser *op;
GtOption *option;
SpeccheckArguments *arguments = tool_arguments;
/* init */
op = gt_option_parser_new("[options] [GFF3_file ...]",
"Checks spec definition compliance in GFF3 input.");
option = gt_option_new_filename("specfile",
"file with specification definition",
arguments->specfile);
gt_option_parser_add_option(op, option);
gt_option_is_mandatory(option);
option = gt_option_new_bool("colored", "show colored output",
&arguments->colored, true);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("allexpects", "show results counted by "
"expectations instead of by nodes",
&arguments->allexpects, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("provideindex", "provide feature index in "
"specfile namespace (requires O(n) memory for n "
"input features)",
&arguments->provideindex, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("sort", "sort input before checking (requires "
"O(n) memory for n input features)",
&arguments->sort, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("failhard", "stop processing and report runtime "
"errors instead of recording them in the results",
&arguments->fail_hard, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
gt_seqid2file_register_options(op, arguments->s2fi);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
return op;
}
static GtOptionParser *gt_tyr_search_option_parser_new(void *tool_arguments)
{
GtOptionParser *op;
GtOption *option, *optiontyr, *optionqueries;
Tyr_search_options *arguments = tool_arguments;
op = gt_option_parser_new("[options] -tyr tallymer-index -q queryfile0 "
"[queryfile1..] [options]",
"Search a set of k-mers in an index constructed "
"by \"gt tyr mkindex\".");
gt_option_parser_set_mailaddress(op,"<*****@*****.**>");
optiontyr = gt_option_new_string("tyr","specify tallymer-index",
arguments->str_inputindex,
NULL);
gt_option_is_mandatory(optiontyr);
gt_option_parser_add_option(op, optiontyr);
optionqueries = gt_option_new_filenamearray("q","specify query file names",
arguments->queryfilenames);
gt_option_is_mandatory(optionqueries);
gt_option_parser_add_option(op, optionqueries);
option = gt_option_new_string("strand",
"specify the strand to be searched: "
"use f (for forward strand) or "
"p (for reverse complemented strand) or "
"fp (for both); default is f",
arguments->strandspec,
"f");
gt_option_parser_add_option(op, option);
option = gt_option_new_stringarray("output",
"specify output flags "
"(qseqnum, qpos, counts, sequence)",
arguments->showmodespec);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("test", "perform tests to verify program "
"correctness", &arguments->performtest,
false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
return op;
}
static GtOPrval parse_options(int *parsed_args, int argc, const char **argv,
GtError *err)
{
GtOptionParser *op;
GtOPrval oprval;
gt_error_check(err);
op = gt_option_parser_new("file [...]",
"Map the supplied files into memory and "
"read them once.");
gt_option_parser_set_min_args(op, 1);
oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
err);
gt_option_parser_delete(op);
return oprval;
}