simulation_driver.cc

/**
 * @file simulation_driver.cc
 * @author Melissa Ip
 *
 * This file runs simulations using command line inputs and the SimulationModel
 * class. The output file is formatted into two columns. Probability of mutation
 * is the first column and whether the site has a mutation is the second column.
 * Each entry is tab separated and each site is placed on a new line. For
 * example:
 *
 * 1.6732e-10      0
 * 0.00709331      1
 *
 * To compile on Herschel without using cmake and include GSL:
 * c++ -std=c++11 -L/usr/local/lib -lgsl -lgslcblas -lm -I/usr/local/include -o simulation_driver utility.cc read_dependent_data.cc trio_model.cc simulation_model.cc simulation_driver.cc
 *
 * To run this file, provide the following command line inputs:
 * ./simulation_driver <output>.txt <#samples> <coverage> <population mutation rate> <germline mutation rate> <somatic mutation rate>
 */
#include "simulation_model.h"


int main(int argc, const char *argv[]) {
  if (argc < 7) {
    Die("USAGE: simulation_driver <output>.txt <#samples> <coverage> "
        "<population mutation rate> <germline mutation rate> "
        "<somatic mutation rate>");
  }

  const string file_name = argv[1];
  const int experiment_count = atoi(argv[2]);
  const unsigned int coverage = strtoull(argv[3], NULL, 10);
  const double population_mutation_rate = strtod(argv[4], NULL);
  const double germline_mutation_rate = strtod(argv[5], NULL);
  const double somatic_mutation_rate = strtod(argv[6], NULL);
  
  // Sets up simulation parameters and output results.
  SimulationModel sim(coverage,
                      population_mutation_rate,
                      germline_mutation_rate,
                      somatic_mutation_rate);
  sim.Seed();
  sim.WriteProbability(file_name, experiment_count);
  // sim.WriteMutationCounts(file_name, experiment_count);
  // sim.PrintMutationCounts(experiment_count);
  sim.Free();

  return 0;
}