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 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 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 _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 RandomAccel2D::appendOptions(po::options_description &opts)
{
// Accepts a config file and common opts
PositionGenerator::appendOptions(opts);
// Update CLI options
po::options_description local_opts;
local_opts.add_options()
("sigma-accel,a", po::value<double>(),
"Standard deviation of normally-distributed random accelerations")
;
opts.add(local_opts);
// Return valid keys
for (auto &o : local_opts.options())
config_keys_.push_back(o->long_name());
}
po::variables_map LoadConfigurationSettings(int argNumber, char* argsString[], po::options_description& fileConfig)
{
po::positional_options_description p;
p.add("config-file", 1);
po::options_description general = getGeneralConfigFileOptions();
po::options_description cmdline= getCMDLineOptions();
fileConfig.add(general).add(BlobTrackerAlgorithmParams::getTrackerOptions());
po::variables_map vm;
store(po::command_line_parser(argNumber, argsString).options(cmdline).positional(p).allow_unregistered().run(), vm);
notify(vm);
std::string configFileName = vm["config-file"].as<std::string>();
std::string path = getPath(configFileName);
LoadConfigFileinStore(fileConfig, vm, configFileName);
LoadConfigFileinStore(fileConfig, vm, path + vm["filepath-filename"].as<std::string>());
LoadConfigFileinStore(fileConfig, vm, path + vm["tracker-filename"].as<std::string>());
return vm;
}
void _setOptions(po::options_description &desc,
po::positional_options_description &p) {
p.add("kmer-size", 1);
p.add("input-file", -1);
po::options_description opts("EstimateSize Options");
opts.add_options()
("sample-partitions",po::value<long>()->default_value(samplePartitions),"The number of partitions to break up the file")
("max-sample-fraction", po::value<double>()->default_value(maxSampleFraction), "The maximum amount of data to read")
;
desc.add(opts);
KmerSpectrumOptions::_setOptions(desc, p);
MPIOptions::_setOptions(desc, p);
GeneralOptions::_setOptions(desc, p);
KmerBaseOptions::_setOptions(desc, p);
KmerSpectrumOptions::_setOptions(desc, p);
}
foreach(boost::shared_ptr<po::options_description> x, opts_desc){
visible.add(*x);
}
void Recorder::appendOptions(po::options_description &opts)
{
// Common program options
opts.add_options()
("frame-sources,s", po::value< std::vector<std::string> >()->multitoken(),
"The names of the FRAME SOURCES that supply images to save to video.")
("position-sources,p", po::value< std::vector<std::string> >()->multitoken(),
"The names of the POSITION SOURCES that supply object positions "
"to be recorded.")
("config,c", po::value<std::vector<std::string> >()->multitoken(),
"Configuration file/key pair.\n"
"e.g. 'config.toml mykey'")
;
// Update CLI options
po::options_description local_opts;
local_opts.add_options()
("filename,n", po::value<std::string>(),
"The base file name. If not specified, defaults to the SOURCE "
"name.")
("folder,f", po::value<std::string>(),
"The path to the folder to which the video stream and position "
"data will be saved. If not specified, defaults to the "
"current directory.")
("date,d",
"If specified, YYYY-MM-DD-hh-mm-ss_ will be prepended to the "
"filename.")
("allow-overwrite,o",
"If set and save path matches and existing file, the file will "
"be overwritten instead of a incremental numerical index being "
"appended to the file name.")
("fourcc,F", po::value<std::string>(),
"Four character code (https://en.wikipedia.org/wiki/FourCC) used to "
"specify the codec used for AVI video compression. Must be specified as "
"a 4-character string (see http://www.fourcc.org/codecs.php for "
"possible options). Not all valid FOURCC codes will work: it "
"must be implemented by the low level writer. Common values are "
"'DIVX' or 'H264'. Defaults to 'None' indicating uncompressed "
"video.")
("binary-file,b",
"Position data will be written as numpy data file (version 1.0) "
"instead of JSON. Each position data point occupies a single entry "
"in a structured numpy array. Individual position characteristics "
"are described in the arrays dtype.")
("concise-file,c",
"If set and using JSON file format, indeterminate position data fields "
"will not be written e.g. pos_xy will not be written even when "
"pos_ok = false. This means that position objects will be of "
"variable size depending on the validity of whether a position was "
"detected or not, potentially complicating file parsing.")
("interactive", "Start recorder with interactive controls enabled.")
("rpc-endpoint", po::value<std::string>(),
"Yield interactive control of the recorder to a remote ZMQ REQ "
"socket using an interal REP socket with ZMQ style endpoint "
"specifier: '<transport>://<host>:<port>'. For instance, "
"'tcp://*:5555' to specify TCP communication on ports 5555.")
;
opts.add(local_opts);
// Return valid keys
for (auto &o : local_opts.options())
config_keys_.push_back(o->long_name());
}
