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A library for working with phylogenetic and population genetic data.
v0.27.0
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Go to the documentation of this file. 1 #ifndef GENESIS_POPULATION_FUNCTIONS_AFS_ESTIMATE_H_
2 #define GENESIS_POPULATION_FUNCTIONS_AFS_ESTIMATE_H_
47 namespace population {
81 std::vector<bool>
const& alleles,
82 std::vector<unsigned char>
const& phred_scores,
88 std::vector<bool>
const& alleles,
89 std::vector<unsigned char>
const& phred_scores,
90 bool invert_alleles =
false
99 template<
class ForwardIterator>
101 ForwardIterator begin,
111 #endif // include guard
std::vector< unsigned char > phred_scores
std::vector< bool > alleles
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)
Single line/record from a pileup file.
Container namespace for all symbols of genesis in order to keep them separate when used as a library.
void process_conditional_probability(ForwardIterator begin, ForwardIterator end)
Compute the conditional probabilities of AFs. This reimplements process_probCond from Boitard et al.
Helper to store the data of one pileup line/record needed for the Boitard et al Allele Frequency Esti...
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)