void _setOptions(po::options_description &desc,
po::positional_options_description &p) {
po::options_description usage("Usage: DistributedNucleatingAssembly <options> [[--contig-file contigs.fa] [[--input-file input.fq ...]\n\tNote: --contig-file and --input-file can be specified either as a positional argument or within the options");
p.add("contig-file", 1);
p.add("input-file", -1);
desc.add(usage);
po::options_description opts("DistributedNucleatingAssembly Options");
opts.add_options()
("max-iterations", po::value<int>()->default_value(maxIterations), "the maximum number of rounds to extend the set of contigs")
("max-contigs-per-batch", po::value<int>()->default_value(maxContigsPerBatch), "the maximum number of assemblies (per mpi) to gather reads and execute per batch")
("max-contig-length", po::value<int>()->default_value(maxContigLength), "the maximum size of a contig to continue extending");
desc.add(opts);
MatcherInterfaceOptions::_setOptions(desc,p);
KmerMatchOptions::_setOptions(desc,p);
KmerBaseOptions::_setOptions(desc,p);
KmerSpectrumOptions::_setOptions(desc,p);
VmatchOptions::_setOptions(desc,p);
ContigExtenderBaseOptions::_setOptions(desc,p);
NewblerOptions::_setOptions(desc, p);
Cap3Options::_setOptions(desc,p);
MPIOptions::_setOptions(desc,p);
FilterKnownOdditiesOptions::_setOptions(desc,p);
GeneralOptions::_setOptions(desc,p);
};
void inflate_initializer(po::options_description& inflate_desc)
{
UtilityProgramOptions::add_help_suboption(inflate_desc);
UtilityProgramOptions::add_desc_suboption(inflate_desc);
UtilityProgramOptions::add_output_suboption(inflate_desc);
inflate_desc.add_options()("structure,s", po::value<fs::path>()->required(),
"POS.vasp like file you want to "
"increase the boundaries of");
inflate_desc.add_options()("length,l", po::value<std::vector<double>>()->multitoken()->required(),
"amount that each lattice vector will grow (three values "
"corresponding to a, b, and c)");
return;
}
void struc_score_initializer(po::options_description& struc_score_desc)
{
UtilityProgramOptions::add_help_suboption(struc_score_desc);
UtilityProgramOptions::add_output_suboption(struc_score_desc);
struc_score_desc.add_options()("reference,r", po::value<fs::path>()->required(),
"POS.vasp like file to use as reference structure.");
struc_score_desc.add_options()("mappable,m", po::value<std::vector<fs::path>>()->multitoken(),
"POS.vasp like file(s) to map, get structure score for.");
struc_score_desc.add_options()("batch,b", po::value<fs::path>(),
"Batch file containing list of structures files to get structure score for.");
struc_score_desc.add_options()("weight,w", po::value<double>()->default_value(0.5),
"Weight w in structure score: w*lattice_score + (1-w)*basis_score.");
return;
}
void InitOptions(po::options_description& opts, po::positional_options_description&) override {
opts.add_options()
("home", po::value<std::string>()->required(), "home directory")
("proxy,p", po::value<std::string>()->default_value("localhost"), "proxy host")
;
po::options_description indexerOpts("Lister options");
indexerOpts.add_options()
("verbose,v", "use verbose mode")
("chunk-size", po::value<size_t>(), "custom chunk size")
;
opts.add(indexerOpts);
}
void NSCPClient::add_local_options(po::options_description &desc, client::configuration::data_type data) {
desc.add_options()
("no-ssl,n", po::value<bool>()->zero_tokens()->default_value(false)->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_bool_data, &data->recipient, "no ssl", _1)),
"Do not initial an ssl handshake with the server, talk in plaintext.")
("certificate,c", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "certificate", _1)),
"Length of payload (has to be same as on the server)")
("dh", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "dh", _1)),
"Length of payload (has to be same as on the server)")
("certificate-key,k", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "certificate key", _1)),
"Client certificate to use")
("certificate-format", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "certificate format", _1)),
"Client certificate format")
("ca", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "ca", _1)),
"Certificate authority")
("verify", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "verify mode", _1)),
"Client certificate format")
("allowed-ciphers", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "allowed ciphers", _1)),
"Client certificate format")
("ssl,n", po::value<bool>()->zero_tokens()->default_value(false)->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_bool_data, &data->recipient, "ssl", _1)),
"Initial an ssl handshake with the server.")
("timeout", po::value<unsigned int>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_int_data, &data->recipient, "timeout", _1)),
"")
;
}
void options_includes::fill_desc( po::options_description& desc )
{
desc.add_options()
( include_tag, po::value< vector<string> >(&includes)->composing(), include_desc )
( sysincl_tag, po::value< vector<string> >(&sysincls)->composing(), sysincl_desc )
;
}
void SyslogClient::add_local_options(po::options_description &desc, client::configuration::data_type data) {
desc.add_options()
("severity,s", po::value<std::string>()->notifier(boost::bind(&nscapi::functions::destination_container::set_string_data, &data->recipient, "severity", _1)),
"Severity of error message")
("unknown-severity", po::value<std::string>()->notifier(boost::bind(&nscapi::functions::destination_container::set_string_data, &data->recipient, "unknown_severity", _1)),
"Severity of error message")
("ok-severity", po::value<std::string>()->notifier(boost::bind(&nscapi::functions::destination_container::set_string_data, &data->recipient, "ok_severity", _1)),
"Severity of error message")
("warning-severity", po::value<std::string>()->notifier(boost::bind(&nscapi::functions::destination_container::set_string_data, &data->recipient, "warning_severity", _1)),
"Severity of error message")
("critical-severity", po::value<std::string>()->notifier(boost::bind(&nscapi::functions::destination_container::set_string_data, &data->recipient, "critical_severity", _1)),
"Severity of error message")
("facility,f", po::value<std::string>()->notifier(boost::bind(&nscapi::functions::destination_container::set_string_data, &data->recipient, "facility", _1)),
"Facility of error message")
("tag template", po::value<std::string>()->notifier(boost::bind(&nscapi::functions::destination_container::set_string_data, &data->recipient, "tag template", _1)),
"Tag template (TODO)")
("message template", po::value<std::string>()->notifier(boost::bind(&nscapi::functions::destination_container::set_string_data, &data->recipient, "message template", _1)),
"Message template (TODO)")
;
}
// Private methods ----------------------------------
void
EnvironmentOptions::defineMyOptions(po::options_description& optionsDesc) const
{
#ifdef QUESO_MEMORY_DEBUGGING
std::cout << "In EnvOptions::defineMyOptions(), before add_options()" << std::endl;
#endif
optionsDesc.add_options()
(m_option_help.c_str(), "produce help message for environment" )
(m_option_numSubEnvironments.c_str(), po::value<unsigned int>()->default_value(UQ_ENV_NUM_SUB_ENVIRONMENTS_ODV), "number of subEnvironments" )
(m_option_subDisplayFileName.c_str(), po::value<std::string >()->default_value(UQ_ENV_SUB_DISPLAY_FILE_NAME_ODV), "output filename for subscreen writing" )
(m_option_subDisplayAllowAll.c_str(), po::value<bool >()->default_value(UQ_ENV_SUB_DISPLAY_ALLOW_ALL_ODV), "Allow all processors to write to output file" )
(m_option_subDisplayAllowInter0.c_str(), po::value<bool >()->default_value(UQ_ENV_SUB_DISPLAY_ALLOW_INTER0_ODV), "Allow all inter0 nodes to write to output file")
(m_option_subDisplayAllowedSet.c_str(), po::value<std::string >()->default_value(UQ_ENV_SUB_DISPLAY_ALLOWED_SET_ODV), "subEnvs that will write to output file" )
(m_option_displayVerbosity.c_str(), po::value<unsigned int>()->default_value(UQ_ENV_DISPLAY_VERBOSITY_ODV), "set verbosity" )
(m_option_syncVerbosity.c_str(), po::value<unsigned int>()->default_value(UQ_ENV_SYNC_VERBOSITY_ODV), "set sync verbosity" )
(m_option_checkingLevel.c_str(), po::value<unsigned int>()->default_value(UQ_ENV_CHECKING_LEVEL_ODV), "set checking level" )
(m_option_rngType.c_str(), po::value<std::string >()->default_value(UQ_ENV_RNG_TYPE_ODV), "set rngType" )
(m_option_seed.c_str(), po::value<int >()->default_value(UQ_ENV_SEED_ODV), "set seed" )
(m_option_platformName.c_str(), po::value<std::string >()->default_value(UQ_ENV_PLATFORM_NAME_ODV), "platform name" )
(m_option_identifyingString.c_str(), po::value<std::string >()->default_value(UQ_ENV_IDENTIFYING_STRING_ODV), "identifying string" )
//(m_option_numDebugParams.c_str(), po::value<unsigned int>()->default_value(UQ_ENV_NUM_DEBUG_PARAMS_ODV), "set number of debug parameters" )
;
#ifdef QUESO_MEMORY_DEBUGGING
std::cout << "In EnvOptions::defineMyOptions(), after add_options()" << std::endl;
#endif
return;
}
void option_macros::fill_desc( po::options_description& desc ){
desc.add_options()
( define_tag, po::value< vector<string> >(&defines)->composing(), define_desc )
( predef_tag, po::value< vector<string> >(&predefs)->composing(), predef_desc )
( undef_tag , po::value< vector<string> >(&undefs )->composing(), undef_desc )
;
}
// Private methods ---------------------------------
void
uqMonteCarloSGOptionsClass::defineMyOptions(po::options_description& optionsDesc) const
{
optionsDesc.add_options()
(m_option_help.c_str(), "produce help message for Monte Carlo distribution calculator")
(m_option_dataOutputFileName.c_str(), po::value<std::string >()->default_value(UQ_MOC_SG_DATA_OUTPUT_FILE_NAME_ODV ), "name of generic data output file" )
(m_option_dataOutputAllowedSet.c_str(), po::value<std::string >()->default_value(UQ_MOC_SG_DATA_OUTPUT_ALLOWED_SET_ODV ), "subEnvs that will write to generic data output file" )
(m_option_pseq_dataOutputPeriod.c_str(), po::value<unsigned int>()->default_value(UQ_MOC_SG_PSEQ_DATA_OUTPUT_PERIOD_ODV ), "period of message display during param sequence generation" )
(m_option_pseq_dataOutputFileName.c_str(), po::value<std::string >()->default_value(UQ_MOC_SG_PSEQ_DATA_OUTPUT_FILE_NAME_ODV ), "name of data output file for parameters" )
(m_option_pseq_dataOutputFileType.c_str(), po::value<std::string >()->default_value(UQ_MOC_SG_PSEQ_DATA_OUTPUT_FILE_TYPE_ODV ), "type of data output file for parameters" )
(m_option_pseq_dataOutputAllowedSet.c_str(), po::value<std::string >()->default_value(UQ_MOC_SG_PSEQ_DATA_OUTPUT_ALLOWED_SET_ODV), "subEnvs that will write to data output file for parameters" )
#ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
(m_option_pseq_computeStats.c_str(), po::value<bool >()->default_value(UQ_MOC_SG_PSEQ_COMPUTE_STATS_ODV ), "compute statistics on sequence of parameter" )
#endif
(m_option_qseq_dataInputFileName.c_str(), po::value<std::string >()->default_value(UQ_MOC_SG_QSEQ_DATA_INPUT_FILE_NAME_ODV ), "name of data input file for qois" )
(m_option_qseq_dataInputFileType.c_str(), po::value<std::string >()->default_value(UQ_MOC_SG_QSEQ_DATA_INPUT_FILE_TYPE_ODV ), "type of data input file for qois" )
(m_option_qseq_size.c_str(), po::value<unsigned int>()->default_value(UQ_MOC_SG_QSEQ_SIZE_ODV ), "size of qoi sequence" )
(m_option_qseq_displayPeriod.c_str(), po::value<unsigned int>()->default_value(UQ_MOC_SG_QSEQ_DISPLAY_PERIOD_ODV ), "period of message display during qoi sequence generation" )
(m_option_qseq_measureRunTimes.c_str(), po::value<bool >()->default_value(UQ_MOC_SG_QSEQ_MEASURE_RUN_TIMES_ODV ), "measure run times" )
(m_option_qseq_dataOutputPeriod.c_str(), po::value<unsigned int>()->default_value(UQ_MOC_SG_QSEQ_DATA_OUTPUT_PERIOD_ODV ), "period of message display during qoi sequence generation" )
(m_option_qseq_dataOutputFileName.c_str(), po::value<std::string >()->default_value(UQ_MOC_SG_QSEQ_DATA_OUTPUT_FILE_NAME_ODV ), "name of data output file for qois" )
(m_option_qseq_dataOutputFileType.c_str(), po::value<std::string >()->default_value(UQ_MOC_SG_QSEQ_DATA_OUTPUT_FILE_TYPE_ODV ), "type of data output file for qois" )
(m_option_qseq_dataOutputAllowedSet.c_str(), po::value<std::string >()->default_value(UQ_MOC_SG_QSEQ_DATA_OUTPUT_ALLOWED_SET_ODV), "subEnvs that will write to data output file for qois" )
#ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
(m_option_qseq_computeStats.c_str(), po::value<bool >()->default_value(UQ_MOC_SG_QSEQ_COMPUTE_STATS_ODV ), "compute statistics on sequence of qoi" )
#endif
;
return;
}
void options_display_info::fill_desc( po::options_description& desc )
{
desc.add_options()
( help_tag, help_desc)
( version_tag, version_desc )
;
pdesc = &desc;
}
void InitOptions(po::options_description& opts, po::positional_options_description&) override {
opts.add_options()
("path,p", po::value<std::string>()->default_value("."), "path to a root directory")
("index,i", po::value<std::string>()->required(), "index path prefix")
;
po::options_description listerOpts("Lister options");
listerOpts.add_options()
("verbose,v", "use verbose mode")
("recursive,r", po::value<bool>()->default_value(true), "traverse recursively")
("hidden", "do not ignore hidden directories/files")
("max-depth", po::value<int>()->default_value(-1), "max recursion depth")
;
opts.add(listerOpts);
}
void runner::register_options(const po::options_description& options)
{
assert(m_impl);
const auto& opt = options.options();
for (const auto& o: opt)
m_impl->m_options_description.add(o);
}
void applystrain_initializer(po::options_description& applystrain_desc)
{
UtilityProgramOptions::add_help_suboption(applystrain_desc);
UtilityProgramOptions::add_output_suboption(applystrain_desc);
applystrain_desc.add_options()("structure,s", po::value<fs::path>()->required(),
"POS.vasp like file that you want to apply strain to.");
applystrain_desc.add_options()("mode,m", po::value<std::string>()->default_value("GL"),
"Accepts strain convention as mode ('GL' [Green-Lagrange, default], 'EA' "
"[Euler-Almansi], 'B' [Biot], or 'H' [Hencky])."
" Also accepts 'F' [Deformation] as an argument to apply a deformation tensor");
applystrain_desc.add_options()("tensor,t", po::value<fs::path>()->required(),
"Path to a file with strain tensor."
" Unrolled strain should be provided for GL, B, H, EA modes."
" Ordered as E(0,0) E(1,1) E(2,2) E(1,2) E(0,2) E(0,1)."
" Takes a 3X3 matrix for F (Deformation) mode.");
return;
}
void Viewer<T>::appendOptions(po::options_description &opts)
{
// Common program options
opts.add_options()
("config,c", po::value<std::vector<std::string> >()->multitoken(),
"Configuration file/key pair.\n"
"e.g. 'config.toml mykey'")
;
}
void Application::buildOptions(po::options_description &desc)
{
desc.add_options()
("camera,c", po::value(&m_OptCameraName)->default_value(CVTRACKER_DEFAULT_CAMERA), "specific camera to calibrate")
("width,w", po::value(&m_OptCameraWidth)->default_value(320), "camera capture width")
("height,h", po::value(&m_OptCameraHeight)->default_value(240), "camera capture height")
("rate,r", po::value(&m_OptCameraRate)->default_value(25), "camera capture rate")
("tracker,t", po::value(&m_OptTracker)->default_value(CVTRACKER_DEFAULT_TRACKER), "tracker to use");
}
void options_io::fill_desc( po::options_description& desc )
{
desc.add_options()
( in_tag, po::value<string>(&input_file), in_desc )
( out_tag, po::value<string>(&output_file_name), out_desc )
( dump_ir_tag, po::value<string>(&dump_ir), dump_ir_desc )
( export_as_tag,po::value<string>(&fmt_str), export_as_desc )
( lang_tag, po::value<string>(&lang_str), lang_desc )
;
}
//////////////////////////////////////////////////////////////////////////
// options global
void options_global::fill_desc( po::options_description& desc )
{
desc.add_options()
(
"detail-level", po::value<string>(&detail_str),
"Specify the detail level of compiler output."
"The optional items are: quite(q), brief(b), normal(n), verbose(v)."
"Default is normal"
);
}
//==============================================================================
void CC_Base::init_options(po::options_description &desc)
{
desc.add_options()
("help,h", "produce help message");
desc.add_options()
("log", po::value<String>(&option_log_name_)->implicit_value(""),
"create log of all operations");
desc.add_options()
("device,d", po::value<String>(&option_device_address_),
"set programmer deivce usb address 'bus:device'");
desc.add_options()
("fast,f", "set fast debug interface speed (by default: slow)"); //TODO made fast by default
desc.add_options()
("name,n", po::value<String>(&option_unit_name_),
"specify target name e.g. CC2530 etc.");
}
void DistributedClient::add_local_options(po::options_description &desc, client::configuration::data_type data) {
desc.add_options()
("certificate,c", po::value<std::string>()->notifier(boost::bind(&nscapi::functions::destination_container::set_string_data, &data->recipient, "certificate", _1)),
"Length of payload (has to be same as on the server)")
/*
("no-ssl,n", po::value<bool>(&command_data.no_ssl)->zero_tokens()->default_value(false), "Do not initial an ssl handshake with the server, talk in plain text.")
("cert,c", po::value<std::wstring>(&command_data.cert)->default_value(cert_), "Certificate to use.")
*/
;
}
inline void opt_stp_desc(po::options_description &desc)
{
desc.add_options()
("dt", po::value<string>()->default_value("auto"), "time step [s]")
("dt_out", po::value<string>(), "output interval [s] (if dt == auto)")
("t_max", po::value<string>(), "time of simulation [s] (if dt == auto)")
("nt", po::value<unsigned long>(), "number of time steps [1] (if dt != auto)")
("nout", po::value<int>(), "output interval [dt] (if dt != auto)");
}
void InfiniteDimensionalMCMCSamplerOptions::defineMyOptions(
po::options_description & optionsDesc) const
{
optionsDesc.add_options()
(m_option_help.c_str(), "produce help message for infinite dimensional sampler")
(m_option_dataOutputDirName.c_str(), po::value<std::string>()->default_value(UQ_INF_DATA_OUTPUT_DIR_NAME_ODV), "name of data output dir")
(m_option_dataOutputFileName.c_str(), po::value<std::string>()->default_value(UQ_INF_DATA_OUTPUT_FILE_NAME_ODV), "name of data output file (HDF5)")
(m_option_num_iters.c_str(), po::value<int>()->default_value(UQ_INF_NUM_ITERS_ODV), "number of mcmc iterations to do")
(m_option_save_freq.c_str(), po::value<int>()->default_value(UQ_INF_SAVE_FREQ_ODV), "the frequency at which to save the chain state")
(m_option_rwmh_step.c_str(), po::value<double>()->default_value(UQ_INF_RWMH_STEP_ODV), "the step-size in the random-walk Metropolis proposal");
return;
}
void SMTPClient::add_local_options(po::options_description &desc, client::configuration::data_type data) {
desc.add_options()
("sender", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "sender", _1)),
"Length of payload (has to be same as on the server)")
("recipient", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "recipient", _1)),
"Length of payload (has to be same as on the server)")
("template", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "template", _1)),
"Do not initial an ssl handshake with the server, talk in plaintext.")
;
}
options() : descriptions("Allowed Options") {
descriptions.add_options()
("help,h", "Produce help message.")
("input-file,i", po::value<std::string>(), "File to open as input")
#ifdef HAVE_PSTREAMS
("pipe-comm,p", "Communicate to merit function on stdout/stderr instead "
"of using input/output files. ")
#endif
("num-threads,n", po::value<unsigned int>()->default_value(2u),
"Use up to <value> threads. This can also be "
"specified by the environment variable\n"
"NUM_PTHREADS")
;
}
virtual void pluginRegisterHelp(po::options_description& desc)
{
desc.add_options()
("steps,s", po::value<uint32_t > (&runSteps), "Simulation steps")
("percent,p", po::value<uint16_t > (&progress)->default_value(5),
"Print time statistics after p percent to stdout")
("restart", po::value<bool>(&restartRequested)->zero_tokens(), "Restart simulation")
("restart-directory", po::value<std::string>(&restartDirectory)->default_value(restartDirectory),
"Directory containing checkpoints for a restart")
("restart-step", po::value<int32_t>(&restartStep), "Checkpoint step to restart from")
("checkpoints", po::value<uint32_t>(&checkpointPeriod), "Period for checkpoint creation")
("checkpoint-directory", po::value<std::string>(&checkpointDirectory)->default_value(checkpointDirectory),
"Directory for checkpoints");
}
void pluginRegisterHelp(po::options_description& desc)
{
/* register command line parameters for your plugin */
desc.add_options()
("resourceLog.period", po::value<uint32_t>(¬ifyPeriod)->default_value(0),
"Enable ResourceLog plugin [for each n-th step]")
("resourceLog.prefix", po::value<std::string>(&outputFilePrefix)->default_value("resourceLog_"),
"Set the filename prefix for output file if a filestream was selected")
("resourceLog.stream", po::value<std::string>(&streamType)->default_value("file"),
"Output stream [stdout, stderr, file]")
("resourceLog.properties", po::value<std::vector<std::string> >(&properties)->multitoken(),
"List of properties to log [rank, position, currentStep, cellCount, particleCount]")
("resourceLog.format", po::value<std::string>(&outputFormat)->default_value("json"),
"Output format of log (pp for pretty print) [json, jsonpp, xml, xmlpp]");
}
void testConfigOptions(po::options_description &desc)
{
// Add test-specific options
desc.add_options()
("vc", po::value<int>()->default_value(0), "Channel (0=VA, 1=VL0, 2=VH0, 3=VH1)")
("rdline-s", po::value<bool>()->default_value(true), "Emit read requests with shared cache hint")
("wrline-m", po::value<bool>()->default_value(true), "Emit write requests with modified cache hint")
("mcl", po::value<int>()->default_value(1), "Multi-line requests (0 for random sizes)")
("min-stride", po::value<int>()->default_value(0), "Minimum stride value")
("max-stride", po::value<int>()->default_value(128), "Maximum stride value")
("tc", po::value<int>()->default_value(10000000), "Test length (cycles)")
("ts", po::value<int>()->default_value(0), "Test length (seconds)")
("enable-warmup", po::value<bool>()->default_value(true), "Warm up VTP's TLB")
("test-mode", po::value<bool>()->default_value(false), "Generate simple memory patterns for testing address logic")
;
}
void _setOptions(po::options_description &desc, po::positional_options_description &p) {
// override the default output format!
// set options specific to this program
p.add("input-file", -1);
po::options_description opts("Fastq to Fasta Options");
opts.add_options()
("split-pairs", po::value<bool>()->default_value(splitPairs), "if set, pairs will be directed into separate files")
("split-size-mbase", po::value<int>()->default_value(splitSizeMbase), "maximum size of output fastas. requires --output-file");
desc.add(opts);
GeneralOptions::getOptions()._setOptions(desc, p);
}
void _setOptions(po::options_description &desc, po::positional_options_description &p) {
p.add("output-bam", 1);
p.add("input-bams", -1);
po::options_description opts("BamSort-P <options> output.bam input.bam [...]\n\nOptions");
opts.add_options()
("output-bam", po::value<std::string>())
("input-bams", po::value<FileListType>())
("unmapped-read-pairs", po::value<std::string>()->default_value(unmappedReadPairs), "gzipped file to place unmapped read Pairs Fastqs (can be same as --unmapped-reads)")
("unmapped-reads", po::value<std::string>()->default_value(unmappedReads), "gzipped file to place unmapped reads Fastqs (can be same as --unmapped-read-pairs)")
("keep-unmapped-paired-read", po::value<bool>()->default_value(keepUnmappedPairedRead), "if unmapped-read-pairs file is specified, keep an unmapped read in the bam if its pair is mapped")
("num-partitions", po::value<int>()->default_value(numPartitions), "The number of alignment-index partitions to merge. Input bams expected to come ordered grouped by in batches of num-partitions where each group has the exact same read counts in the exact same order");
desc.add(opts);
GeneralOptions::_setOptions(desc, p);
// Other *::_setOptions(desc,p);
}
void NRDPClient::add_local_options(po::options_description &desc, client::configuration::data_type data) {
desc.add_options()
("key", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "token", _1)),
"The security token")
("password", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "token", _1)),
"The security token")
("source-host", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->host_self, "host", _1)),
"Source/sender host name (default is auto which means use the name of the actual host)")
("sender-host", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->host_self, "host", _1)),
"Source/sender host name (default is auto which means use the name of the actual host)")
("token", po::value<std::string>()->notifier(boost::bind(&nscapi::protobuf::functions::destination_container::set_string_data, &data->recipient, "token", _1)),
"The security token")
;
}