libsequence  1.9.5
FragmentsRescaling.hpp
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1 
12 #ifndef __SEQUENCE_COALESCENT_FRAGMENTS_RESCALING_HPP__
13 #define __SEQUENCE_COALESCENT_FRAGMENTS_RESCALING_HPP__
14 
15 #include <Sequence/Coalescent/SimTypes.hpp>
16 #include <vector>
17 #include <utility>
18 
19 namespace Sequence
20 {
21  class SimData; //fwd declaration
22  namespace coalsim {
23  int sample_length( const std::vector< std::pair<int,int> > & fragments );
24  int total_length( const std::vector< std::pair<int,int> > & fragments );
25  void calculate_scales(const std::vector< std::pair<int,int> > & fragments,
26  std::vector< std::pair<double,double> > * sample_scale,
27  std::vector< std::pair<double,double> > * mutation_scale );
28  void rescale_mutation_positions(Sequence::SimData * d,
29  const std::vector< std::pair<double,double> > & sample_scale,
30  const std::vector< std::pair<double,double> > & mutation_scale )__attribute__((deprecated));
31  void rescale_arg( arg * sample_history,
32  const std::vector< std::pair<int,int> > & fragments );
33  double integrate_genetic_map( const std::vector<chromosome> & sample,
34  const int & current_nsam,
35  const std::vector<double> & genetic_map,
36  std::vector<double> * reclens);
37  }
38 }
39 #endif
Sequence::coalsim::calculate_scales
void calculate_scales(const std::vector< std::pair< int, int > > &fragments, std::vector< std::pair< double, double > > *sample_scale, std::vector< std::pair< double, double > > *mutation_scale)
This is a helper function that rescales physical distance in base pairs to continuous distance on the...
Definition: CoalescentFragmentsRescaling.cc:64
Sequence::coalsim::total_length
int total_length(const std::vector< std::pair< int, int > > &fragments)
When simulating partially linked regions, return the total length of the region.
Definition: CoalescentFragmentsRescaling.cc:48
Sequence::coalsim::arg
std::list< marginal > arg
Ancestral Recombination Graph.
Definition: SimTypes.hpp:217
Sequence
The namespace in which this library resides.
SimTypes.hpp
declaration of types for coalescent simulation
Sequence::__attribute__
class __attribute__((deprecated)) FST
Functor to count the number of states, excluding gaps and missing data, in a range of characters...
Definition: FST.hpp:41
Sequence::coalsim::rescale_mutation_positions
void rescale_mutation_positions(Sequence::SimData *d, const std::vector< std::pair< double, double > > &sample_scale, const std::vector< std::pair< double, double > > &mutation_scale) __attribute__((deprecated))
Rescales the positions of the mutations in d from the scale given in sample_scale to that given in mu...
Definition: CoalescentFragmentsRescaling.cc:107
Sequence::coalsim::integrate_genetic_map
double integrate_genetic_map(const std::vector< chromosome > &sample, const int &current_nsam, const std::vector< double > &genetic_map, std::vector< double > *reclens)
When simulating non-uniform recombination rates, the probability of recombination at each point in th...
Definition: CoalescentFragmentsRescaling.cc:168
Sequence::SimData
Data from coalescent simulations.
Sequence::coalsim::sample_length
int sample_length(const std::vector< std::pair< int, int > > &fragments)
When simulating partially linked regions, return the total length of sample material that we are simu...
Definition: CoalescentFragmentsRescaling.cc:32
Sequence::coalsim::rescale_arg
void rescale_arg(arg *sample_history, const std::vector< std::pair< int, int > > &fragments)
Rescales the beginnings of marginal trees in an ancestral recombination graph from a genetic scale to...
Definition: CoalescentFragmentsRescaling.cc:136