A library for working with phylogenetic data.
v0.25.0
afs_estimate.hpp File Reference
#include "genesis/population/formats/simple_pileup_reader.hpp"
#include <string>
#include <vector>

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Classes

struct  AfsPileupRecord
 Helper to store the data of one pileup line/record needed for the Boitard et al Allele Frequency Estimation computation. More...
 

Namespaces

 genesis
 Container namespace for all symbols of genesis in order to keep them separate when used as a library.
 
 genesis::population
 

Functions

AfsPileupRecord convert_to_afs_pileup_record (SimplePileupReader::Record const &record)
 
std::vector< double > prob_cond_true_freq (size_t n, std::vector< bool > const &alleles, std::vector< unsigned char > const &phred_scores, bool unfolded)
 
std::vector< double > prob_cond_true_freq_unfolded (size_t n, std::vector< bool > const &alleles, std::vector< unsigned char > const &phred_scores, bool invert_alleles)
 
template<class ForwardIterator >
void process_conditional_probability (ForwardIterator begin, ForwardIterator end)
 Compute the conditional probabilities of AFs. This reimplements process_probCond from Boitard et al. More...