WhichNullRowsApplication.cpp
b2cb3d77d7e8master

WhichNullRowsApplication.cpp
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			#include <WhichNullRowsApplication.hpp>

			#include <vector>

			#include <boost/program_options.hpp>

			#include <Matrix2D.hpp>


			namespace po = boost::program_options ;



			WhichNullRowsApplication::WhichNullRowsApplication(int argn, char** argv)
			:file_matrix(""), runnable("")
			{ this->parseOptions(argn, argv) ; }

			int WhichNullRowsApplication::run()
			{
			if(this->runnable)
			{ Matrix2D<int> m(this->file_matrix) ;

			std::vector<size_t> null_rows ;

			for(size_t i=0; i<m.get_nrow(); i++)
			{ bool null_row = true ;
			for(size_t j=0; j<m.get_ncol(); j++)
			{ // this row has signal
			if(m(i,j) != 0)
			{ null_row = false ;
			break ;
			}
			}
			if(null_row)
			{ null_rows.push_back(i) ; }
			}

			// clean memory
			m = Matrix2D<int>() ;

			// put the vector into a single column matrix
			// to use the << operator
			Matrix2D<size_t> rows(null_rows.size(), 1) ;
			for(size_t i=0; i< null_rows.size(); i++)
			{ rows(i,0) = null_rows[i] ; }

			std::cout << rows << std::endl ;

			return EXIT_SUCCESS ;
			}
			else
			{ return EXIT_FAILURE; }
			}

			void WhichNullRowsApplication::parseOptions(int argn, char** argv)
			{
			// no option to parse
			if(argv == nullptr)
			{ std::string message = "no options to parse!" ;
			throw std::invalid_argument(message) ;
			}

			// help messages
			std::string desc_msg = "\n"
			"WhichNullRow reads a 2D matrix file in text format and\n"
			"returns the index (0-based) of the rows with no signal.\n\n" ;
			std::string opt_help_msg = "Produces this help message." ;
			std::string opt_file_mat_msg = "The path to the 2D matrix file." ;

			// option parser
			boost::program_options::variables_map vm ;
			boost::program_options::options_description desc(desc_msg) ;

			desc.add_options()
			("help,h", opt_help_msg.c_str())

			("mat", po::value<std::string>(&(this->file_matrix)), opt_file_mat_msg.c_str()) ;

			// parse
			try
			{ po::store(po::parse_command_line(argn, argv, desc), vm) ;
			po::notify(vm) ;
			}
			catch(std::invalid_argument& e)
			{ std::string msg = std::string("Error! Invalid option given!\n") + std::string(e.what()) ;
			throw std::invalid_argument(msg) ;
			}
			catch(...)
			{ throw std::invalid_argument("An unknown error occured while parsing the options") ; }

			bool help = vm.count("help") ;

			// checks unproper option settings
			if(this->file_matrix == "" and
			(not help))
			{ std::string msg("Error! No input file was given (--mat)!") ;
			throw std::invalid_argument(msg) ;
			}

			// help invoked, run() cannot be invoked
			if(help)
			{ std::cout << desc << std::endl ;
			this->runnable = false ;
			return ;
			}
			// everything fine, run() can be called
			else
			{ this->runnable = true ;
			return ;
			}
			}

			int main(int argn, char** argv)
			{ WhichNullRowsApplication app(argn, argv) ;
			return app.run() ;
			}

scATAC-seq/src/Applications/WhichNullRowsApplication.cppb2cb3d77d7e8master

WhichNullRowsApplication.cppView Options

scATAC-seq/src/Applications/WhichNullRowsApplication.cpp
b2cb3d77d7e8master

WhichNullRowsApplication.cpp
View Options