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/*
* combineCmdLine.cpp
* Parses cmd line options for combineKmers
*
*/
#include "combineKmers.hpp"
namespace po = boost::program_options; // Save some typing
// Parse command line options using boost program options
int parseCommandLine (int argc, char *argv[], po::variables_map& vm)
{
int failed = 0;
//Required options
po::options_description required("Required options");
required.add_options()
("samples,r", po::value<std::string>()->required(), "file with tab separated sample name and kmer file")
("output,o", po::value<std::string>()->required(), "output file prefix");
po::options_description other("Other options");
other.add_options()
("min_samples", po::value<int>()->default_value(1), "minimum number of samples kmer must occur in to be printed")
("help,h", "full help message");
po::options_description all;
all.add(required).add(other);
try
{
po::store(po::command_line_parser(argc, argv).options(all).run(), vm);
if (vm.count("help"))
{
printHelp(all);
failed = 1;
}
else
{
po::notify(vm);
failed = 0;
}
}
catch (po::error& e)
{
// Report errors from boost library
std::cerr << "Error in command line input: " << e.what() << "\n";
std::cerr << "Run 'combineKmers --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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