classics.hpp File Reference

"Classic" summaries of variation data. More...

#include <Sequence/VariantMatrix.hpp>
#include <Sequence/AlleleCountMatrix.hpp>
#include "thetapi.hpp"
#include "thetaw.hpp"
#include "thetah.hpp"
#include "thetal.hpp"
#include "nvariablesites.hpp"
#include "allele_counts.hpp"

Go to the source code of this file.

Namespaces
	Sequence
	The namespace in which this library resides.

Functions
double	Sequence::tajd (const AlleleCountMatrix &ac)
	Tajima's D. More...
double	Sequence::hprime (const AlleleCountMatrix &ac, const std::int8_t refstate)
double	Sequence::hprime (const AlleleCountMatrix &m, const std::vector< std::int8_t > &refstates)
double	Sequence::faywuh (const AlleleCountMatrix &ac, const std::int8_t refstate)
	Fay and Wu's H. More...
double	Sequence::faywuh (const AlleleCountMatrix &ac, const std::vector< std::int8_t > &refstates)
	Fay and Wu's H. More...
std::vector< std::int32_t >	Sequence::difference_matrix (const VariantMatrix &m)
	Calculate number of differences between all samples. More...
std::vector< std::int32_t >	Sequence::is_different_matrix (const VariantMatrix &m)
std::vector< std::int32_t >	Sequence::label_haplotypes (const VariantMatrix &m)
	Assign a unique label to each haplotype. More...
std::int32_t	Sequence::number_of_haplotypes (const VariantMatrix &m)
	Calculate the number of haplotypes in a sample. More...
double	Sequence::haplotype_diversity (const VariantMatrix &m)
	Calculate the haplotype diversity of a sample. More...
std::int32_t	Sequence::rmin (const VariantMatrix &m)

Detailed Description

"Classic" summaries of variation data.

Definition in file classics.hpp.