testClassicSummstats.cc File Reference

unit tests for pop gen summary statistics More...

#include <cmath>
#include <algorithm>
#include <set>
#include <string>
#include <vector>
#include <iostream>
#include <Sequence/VariantMatrix.hpp>
#include <Sequence/VariantMatrixViews.hpp>
#include <Sequence/summstats/classics.hpp>
#include "VariantMatrixFixture.hpp"
#include <boost/test/unit_test.hpp>

Go to the source code of this file.

Functions
static double	manual_pi (const Sequence::VariantMatrix &m)
static double	manual_thetah (const Sequence::VariantMatrix &m, const std::int8_t refstate)
	BOOST_AUTO_TEST_CASE (test_thetapi)
	BOOST_CHECK_CLOSE (pi, manual, 1e-6)
	BOOST_AUTO_TEST_CASE (test_num_poly_sites)
	BOOST_AUTO_TEST_CASE (test_total_num_mutations)
	BOOST_AUTO_TEST_CASE (test_nbiallelic_sites)
	BOOST_AUTO_TEST_CASE (test_count_alleles)
	for (int i=1;i< m.nsam;++i)
	BOOST_CHECK_CLOSE (w, manual, 1e-6)
	BOOST_CHECK_CLOSE (h0, m0, 1e-6)
	BOOST_CHECK_CLOSE (h1, m1, 1e-6)
	BOOST_CHECK_EQUAL (fwh+h, pi)
	BOOST_REQUIRE_EQUAL (pi - h, fwh)
	BOOST_AUTO_TEST_CASE (test_thetah_multiple_derived_states)
	BOOST_AUTO_TEST_CASE (test_num_haplotypes)
	BOOST_AUTO_TEST_CASE (test_unique_hap_at_any_index)
	BOOST_AUTO_TEST_CASE (test_haplotype_diversity)
	BOOST_AUTO_TEST_CASE (test_rmin)

Variables
auto	manual = manual_pi(m)
double	S = m.nsites
double	d = 0.0
auto	h1 = Sequence::thetah(c, 1)
auto	m0 = manual_thetah(m, 0)
auto	m1 = manual_thetah(m, 1)
auto	pi = Sequence::thetapi(c)
auto	fwh = Sequence::faywuh(c, 0)

Detailed Description

unit tests for pop gen summary statistics

Definition in file testClassicSummstats.cc.