Coalescent/Recombination.hpp

#ifndef __SEQUENCE_COALESCENT_RECOMBINATION_HPP__
#define __SEQUENCE_COALESCENT_RECOMBINATION_HPP__

#include <Sequence/Coalescent/SimTypes.hpp>
namespace Sequence
{
  namespace coalsim {
    int crossover( const int & current_nsam,
                   const int & chromo,
                   const int & pos,
                   std::vector<chromosome> * sample,
                   arg * sample_history);

    std::pair<int,int> pick_uniform_spot(const double & random_01,
                                         const int & nlinks,
                                         std::vector<chromosome>::const_iterator sample_begin,
                                         const unsigned & current_nsam);

    template<typename uniform01_generator>
    std::pair<int,int> pick_spot( uniform01_generator & uni01,
                                  const double & total_reclen,
                                  const std::vector<double> & reclens,
                                  std::vector<chromosome>::const_iterator sample_begin,
                                  const unsigned & current_nsam,
                                  const double * rec_map);

    template<typename uniform01_generator>
    std::pair<int,int> pick_spot( const uniform01_generator & uni01,
                                  const double & total_reclen,
                                  const std::vector<double> & reclens,
                                  std::vector<chromosome>::const_iterator sample_begin,
                                  const unsigned & current_nsam,
                                  const double * rec_map);
  }
}
#endif
#include <Sequence/Coalescent/bits/Recombination.tcc>