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/*
* File: seerCmdLine.cpp
*
* Reads command line input to seer using boost
* program options
*
*/
#include "seer.hpp"
namespace po = boost::program_options; // Save some typing
// Use boost::program_options to parse command line input
// This does pretty much all the parameter checking needed
int parseCommandLine (int argc, char *argv[], po::variables_map& vm)
{
int failed = 0;
//Required options
po::options_description required("Required options");
required.add_options()
("kmers,k", po::value<std::string>()->required(), "dsm kmer output file")
("pheno,p", po::value<std::string>()->required(), ".pheno metadata");
// kmds options
po::options_description covar("Covariate options");
covar.add_options()
("struct", po::value<std::string>(), "mds values from kmds")
("covar_file", po::value<std::string>(), "file containing covariates")
("covar_list", po::value<std::string>(), "list of columns covariates to use. Format is 1,2q,3 (use q for quantitative)");
//Optional filtering parameters
//NB pval cutoffs are strings for display, and are converted to floats later
po::options_description performance("Performance options");
performance.add_options()
("threads", po::value<int>()->default_value(1), ("number of threads. Suggested: " + std::to_string(std::thread::hardware_concurrency())).c_str());
//Optional filtering parameters
//NB pval cutoffs are strings for display, and are converted to floats later
po::options_description filtering("Filtering options");
filtering.add_options()
("no_filtering", "turn off all filtering and perform tests on all kmers input")
("max_length", po::value<long int>()->default_value(max_length_default), "maximum kmer length")
("maf", po::value<double>()->default_value(maf_default), "minimum kmer frequency")
("min_words", po::value<int>(), "minimum kmer occurences. Overrides --maf")
("chisq", po::value<std::string>()->default_value(chisq_default), "p-value threshold for initial chi squared test. Set to 1 to show all")
("pval", po::value<std::string>()->default_value(pval_default), "p-value threshold for final logistic test. Set to 1 to show all");
po::options_description other("Other options");
other.add_options()
("print_samples", "print lists of samples significant kmers were found in")
("version", "prints version and exits")
("help,h", "full help message");
po::options_description all;
all.add(required).add(covar).add(performance).add(filtering).add(other);
try
{
po::store(po::command_line_parser(argc, argv).options(all).run(), vm);
if (vm.count("help"))
{
printHelp(all);
failed = 1;
}
else if (vm.count("version"))
{
std::cout << VERSION << std::endl;
failed = 1;
}
else
{
po::notify(vm);
failed = 0;
// Check input files exist, and can stat
if (!fileStat(vm["kmers"].as<std::string>()) || !fileStat(vm["pheno"].as<std::string>()))
{
failed = 1;
}
else if (vm.count("struct") && !fileStat(vm["struct"].as<std::string>()))
{
failed = 1;
}
}
}
catch (po::error& e)
{
// Report errors from boost library
std::cerr << "Error in command line input: " << e.what() << "\n";
std::cerr << "Run 'seer --help' for full option listing\n\n";
std::cerr << required << "\n" << other << "\n";
failed = 1;
}
return failed;
}
// Print long help message
void printHelp(po::options_description& help)
{
std::cerr << help << "\n";
}
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