fst_cathedral.hpp File Reference

#include "genesis/population/stream/variant_input_stream.hpp"
#include "genesis/population/function/fst_pool_processor.hpp"
#include "genesis/population/function/fst_pool_unbiased.hpp"
#include "genesis/population/plotting/cathedral_plot.hpp"
#include "genesis/sequence/sequence_dict.hpp"
#include "genesis/utils/containers/matrix.hpp"
#include "genesis/utils/math/compensated_sum.hpp"
#include <cassert>
#include <cmath>
#include <stdexcept>
#include <string>
#include <vector>

Go to the source code of this file.

Classes
class	FstCathedralAccumulator
	Accumulate the partial pi values for a given window to produce a cathedral plot. More...
struct	FstCathedralPlotRecord
	Data for making one FST cathedral plot, that is, one pair of samples and one chromosome. More...
struct	FstCathedralPlotRecord::Entry

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

Functions
void	compute_fst_cathedral_matrix (CathedralPlotParameters const &parameters, FstCathedralPlotRecord &record)
	Compute the matrix of values that represents the cathedral plot for FST. More...
std::vector< FstCathedralPlotRecord >	compute_fst_cathedral_records (VariantInputStream &iterator, FstPoolProcessor &processor, FstPoolCalculatorUnbiased::Estimator fst_estimator, std::vector< std::string > const &sample_names=std::vector< std::string >{}, std::shared_ptr< genesis::sequence::SequenceDict > const &sequence_dict=nullptr)
	Compute the components of per-position FST data for all pairs of samples in the given processor, for the chromosomes in the given input iterator. More...
std::vector< FstCathedralPlotRecord >	compute_fst_cathedral_records_for_chromosome (VariantInputStream::Iterator &iterator, FstPoolProcessor &processor, FstPoolCalculatorUnbiased::Estimator fst_estimator, std::vector< std::string > const &sample_names=std::vector< std::string >{}, std::shared_ptr< genesis::sequence::SequenceDict > const &sequence_dict=nullptr)
	Compute the components of per-position FST data for all pairs of samples in the given processor, for the current chromosome in the given input iterator. More...
genesis::utils::JsonDocument	fst_cathedral_plot_record_to_json_document (FstCathedralPlotRecord const &record)
	Get a user-readable description of the data of a FstCathedralPlotRecord as a JsonDocument. More...