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_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_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 OPrval parse_options(int *parsed_args, int argc, const char **argv,
GtError *err)
{
GtOptionParser *op;
OPrval oprval;
op = gt_option_parser_new("[GFF3_file ...]",
"Parse GFF3 file(s) and show it as "
"GTF2.2.");
/* parse */
gt_option_parser_set_max_args(op, 1);
oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
err);
gt_option_parser_delete(op);
return oprval;
}
static GtOPrval parse_env_options(int argc, const char **argv, GtError *err)
{
GtOptionParser *op;
GtOption *o;
GtOPrval oprval;
op = gt_option_parser_new("GT_ENV_OPTIONS='[option ...]' ...",
"Parse the options contained in the "
"environment variable GT_ENV_OPTIONS.");
o = gt_option_new_bool("spacepeak", "show space peak on stdout upon deletion",
&spacepeak, false);
gt_option_parser_add_option(op, o);
o = gt_option_new_bool("showtime", "enable output for run-time statistics",
&showtime, false);
gt_option_parser_add_option(op, o);
gt_option_parser_set_max_args(op, 0);
oprval = gt_option_parser_parse(op, NULL, argc, argv, gt_versionfunc, err);
gt_option_parser_delete(op);
return oprval;
}
static GtOptionParser* gt_readjoiner_cnttest_option_parser_new(
void *tool_arguments)
{
GtReadjoinerCnttestArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("-readset [option ...]",
"Test/development tool for readjoiner containments filtering.");
/* -readset */
option = gt_option_new_string("readset", "specify the readset name",
arguments->readset, NULL);
gt_option_parser_add_option(op, option);
gt_option_is_mandatory(option);
/* -test */
option = gt_option_new_string("test",
"select among the available tests:\n"
"showlist: show content of an cnt list (input: cntlist)\n"
"bruteforce: memcmp reads vs all suffixes and prefixes (input: encseq)\n"
"kmp: variant of Knuth-Morris-Pratt (input: encseq)\n"
"esa: own esa-based algorithm (input: esa)",
arguments->teststr, NULL);
gt_option_parser_add_option(op, option);
gt_option_is_mandatory(option);
/* -singlestrand */
option = gt_option_new_bool("singlestrand", "do not use reads "
"reverse complements", &arguments->singlestrand, false);
gt_option_parser_add_option(op, option);
/* -v */
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
gt_option_parser_set_max_args(op, 0);
return op;
}
static GtOptionParser* gt_bed_to_gff3_option_parser_new(void *tool_arguments)
{
BEDToGFF3Arguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *o;
op = gt_option_parser_new("[bed_file]",
"Parse BED file and show it as GFF3.");
o = gt_option_new_string("featuretype", "Set type of parsed BED features",
arguments->feature_type, BED_FEATURE_TYPE);
gt_option_parser_add_option(op, o);
o = gt_option_new_string("thicktype", "Set type of parsed thick BED features",
arguments->thick_feature_type,
BED_THICK_FEATURE_TYPE);
gt_option_parser_add_option(op, o);
o = gt_option_new_string("blocktype", "Set type of parsed BED blocks",
arguments->block_type, BED_BLOCK_TYPE);
gt_option_parser_add_option(op, o);
gt_option_parser_set_max_args(op, 1);
return op;
}
static GtOptionParser* gt_readjoiner_assembly_option_parser_new(
void *tool_arguments)
{
GtReadjoinerAssemblyArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option, *errors_option, *deadend_option, *v_option,
*q_option, *bubble_option, *deadend_depth_option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...]",
"Construct string graph and output contigs.");
/* -readset */
option = gt_option_new_string("readset", "specify the readset name",
arguments->readset, NULL);
gt_option_parser_add_option(op, option);
gt_option_is_mandatory(option);
/* -spmfiles */
option = gt_option_new_uint_min("spmfiles", "number of SPM files to read\n"
"this must be equal to the value of -j for the overlap phase",
&arguments->nspmfiles, 1U, 1U);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -l */
option = gt_option_new_uint_min("l", "specify the minimum SPM length",
&arguments->minmatchlength, 0, 2U);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -depthcutoff */
option = gt_option_new_uint_min("depthcutoff", "specify the minimal "
"number of nodes in a contig",
&arguments->depthcutoff, 3U, 1U);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -lengthcutoff */
option = gt_option_new_uint_min("lengthcutoff", "specify the minimal "
"length of a contig",
&arguments->lengthcutoff, 100U, 1U);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -redtrans */
option = gt_option_new_bool("redtrans", "reduce transitive edges",
&arguments->redtrans, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -errors */
errors_option = gt_option_new_bool("errors", "search graph features which "
"may originate from sequencing errors and remove them",
&arguments->errors, false);
gt_option_is_extended_option(errors_option);
gt_option_parser_add_option(op, errors_option);
/* -bubble */
bubble_option = gt_option_new_uint("bubble", "number of rounds of p-bubble "
"removal to perform", &arguments->bubble, 3U);
gt_option_is_extended_option(bubble_option);
gt_option_imply(bubble_option, errors_option);
gt_option_parser_add_option(op, bubble_option);
/* -deadend */
deadend_option = gt_option_new_uint("deadend", "number of rounds of "
"dead end removal to perform a dead end",
&arguments->deadend, 10U);
gt_option_is_extended_option(deadend_option);
gt_option_imply(deadend_option, errors_option);
gt_option_parser_add_option(op, deadend_option);
/* -deadend-depth */
deadend_depth_option = gt_option_new_uint_min("deadend-depth", "specify the "
"maximal depth of a path to an end-vertex by which the path shall be "
"considered a dead end",
&arguments->deadend_depth, 10U, 1U);
gt_option_is_extended_option(deadend_depth_option);
gt_option_imply(deadend_depth_option, errors_option);
gt_option_parser_add_option(op, deadend_depth_option);
/* -paths2seq */
option = gt_option_new_bool("paths2seq", "read <indexname>"
GT_READJOINER_SUFFIX_CONTIG_PATHS " and write "
"<indexname>" GT_READJOINER_SUFFIX_CONTIGS,
&arguments->paths2seq, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -buffersize */
option = gt_option_new_string("buffersize", "specify size for read buffer"
" of paths2seq phase (in bytes, the keywords 'MB' and 'GB' are allowed)",
arguments->buffersizearg, NULL);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
arguments->refoptionbuffersize = gt_option_ref(option);
/* -vd */
option = gt_option_new_bool("vd", "use verbose descriptions for contigs",
&arguments->vd, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -astat */
option = gt_option_new_bool("astat", "calculate A-statistics for each contig",
&arguments->astat, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -cov */
option = gt_option_new_double("cov", "average coverage value to use for the "
"A-statistics calculation", &arguments->coverage, (double)0);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -copynum */
option = gt_option_new_bool("copynum", "load reads copy numbers list from "
"file for the A-statistics calculation",
&arguments->copynum, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -v */
v_option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, v_option);
/* -q */
q_option = gt_option_new_bool("q", "suppress standard output messages",
&arguments->quiet, false);
gt_option_parser_add_option(op, q_option);
gt_option_exclude(q_option, v_option);
/* -load */
option = gt_option_new_bool("load", "save the string graph from file",
&arguments->load, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -save */
option = gt_option_new_bool("save", "save the string graph to file",
&arguments->save, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -show_contigs_info */
option = gt_option_new_bool("cinfo", "output additional files required "
"for contigs graph construction (eqlen only)",
&arguments->show_contigs_info, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
gt_option_parser_set_max_args(op, 0);
return op;
}
