1 #ifndef SEQUENCE_SUMMSTATS_CLASSICS_HPP__ 4 #define SEQUENCE_SUMMSTATS_CLASSICS_HPP__ 6 #include <Sequence/VariantMatrix.hpp> 7 #include <Sequence/AlleleCountMatrix.hpp> 30 double tajd(
const AlleleCountMatrix& ac);
47 double hprime(
const AlleleCountMatrix& ac,
const std::int8_t refstate);
64 double hprime(
const AlleleCountMatrix& m,
65 const std::vector<std::int8_t>& refstates);
82 double faywuh(
const AlleleCountMatrix& ac,
const std::int8_t refstate);
99 double faywuh(
const AlleleCountMatrix& ac,
100 const std::vector<std::int8_t>& refstates);
211 std::int32_t
rmin(
const VariantMatrix& m);
double hprime(const AlleleCountMatrix &ac, const std::int8_t refstate)
std::int32_t number_of_haplotypes(const VariantMatrix &m)
Calculate the number of haplotypes in a sample.
double tajd(const AlleleCountMatrix &ac)
Tajima's D.
The namespace in which this library resides.
Calculate total numbers of polymorphisms.
std::vector< std::int32_t > label_haplotypes(const VariantMatrix &m)
Assign a unique label to each haplotype.
double faywuh(const AlleleCountMatrix &ac, const std::int8_t refstate)
Fay and Wu's H.
Count alleles at variable sites.
std::int32_t rmin(const VariantMatrix &m)
std::vector< std::int32_t > is_different_matrix(const VariantMatrix &m)
double haplotype_diversity(const VariantMatrix &m)
Calculate the haplotype diversity of a sample.
std::vector< std::int32_t > difference_matrix(const VariantMatrix &m)
Calculate number of differences between all samples.