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EMReadApplication.cpp
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Sun, Apr 28, 13:55

EMReadApplication.cpp
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#include <EMReadApplication.hpp>
#include <EMRead.hpp>
#include <iostream>
#include <string>
#include <stdexcept> // std::invalid_argument
#include <boost/program_options.hpp>
#include <Matrix2D.hpp>
#include <Matrix4D.hpp>
namespace po = boost::program_options ;
EMReadApplication::EMReadApplication(int argn, char** argv)
: file_read(""), file_out(""),
n_class(0), n_iter(0), n_shift(0), flip(false), bckg_class(false),
n_threads(0), seed(""), runnable(true)
{
// parse command line options and set the fields
this->parseOptions(argn, argv) ;
}
int EMReadApplication::run()
{ if(this->runnable)
{ EMRead em(Matrix2D<int>(this->file_read),
this->n_class,
this->n_iter,
this->n_shift,
this->flip,
this->bckg_class,
this->seed,
this->n_threads) ;
em.classify() ;
em.get_post_prob().save(this->file_out) ;
return EXIT_SUCCESS ;
}
else
{ return EXIT_FAILURE ; }
}
void EMReadApplication::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"
"EMRead is a probabilistic partitioning algorithm that \n"
"sofetly assigns genomic regions to classes given the shape \n"
"of the read density over the region. The assignment \n"
"probabilities are returned through stdout.\n\n" ;
std::string opt_help_msg = "Produces this help message." ;
std::string opt_thread_msg = "The number of threads dedicated to parallelize the computations,\n "
"by default 0 (no parallelization)." ;
std::string opt_read_msg = "The path to the file containing the read density data" ;
std::string opt_file_out_msg = "A path to a file in which the assignment probabilities will be saved\n"
"in binary format." ;
std::string opt_iter_msg = "The number of iterations." ;
std::string opt_class_msg = "The number of classes to find." ;
std::string opt_shift_msg = "Enables this number of column of shifting "
"freedom to realign the data. By default, shifting is "
"disabled (equivalent to --shift 1)." ;
std::string opt_flip_msg = "Enables flipping to realign the data.";
std::string opt_bckg_msg = "Adds a class to model the signal background. This class\n"
"contains the mean number of read at each position and\n"
"is never updated." ;
std::string opt_seed_msg = "A value to seed the random number generator.";
// option parser
boost::program_options::variables_map vm ;
boost::program_options::options_description desc(desc_msg) ;
std::string seeding_tmp ;
desc.add_options()
("help,h", opt_help_msg.c_str())
("read", po::value<std::string>(&(this->file_read)), opt_read_msg.c_str())
("out", po::value<std::string>(&(this->file_out)), opt_file_out_msg.c_str())
("iter,i", po::value<size_t>(&(this->n_iter)), opt_iter_msg.c_str())
("class,c", po::value<size_t>(&(this->n_class)), opt_class_msg.c_str())
("shift,s", po::value<size_t>(&(this->n_shift)), opt_shift_msg.c_str())
("flip", opt_flip_msg.c_str())
("bgclass", opt_bckg_msg.c_str())
("seed", po::value<std::string>(&(this->seed)), opt_seed_msg.c_str())
("thread", po::value<std::size_t>(&(this->n_threads)), opt_thread_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_read == "" and
(not help))
{ std::string msg("Error! No data were given (--read)!") ;
throw std::invalid_argument(msg) ;
}
if(this->file_out == "" and
(not help))
{ std::string msg("Error! No output file given (--out)!") ;
throw std::invalid_argument(msg) ;
}
// no iter given -> 1 iter
if(this->n_iter == 0)
{ this->n_iter = 1 ; }
// no shift class given -> 1 class
if(this->n_class == 0)
{ this->n_class = 1 ; }
// no shift given, value of 1 -> no shift
if(this->n_shift == 0)
{ this->n_shift = 1 ; }
// set flip
if(vm.count("flip"))
{ this->flip = true ; }
// set background class
if(vm.count("bgclass"))
{ this->bckg_class = true ; }
// 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)
{ EMReadApplication app(argn, argv) ;
return app.run() ;
}

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