21 #include <Sequence/VariantMatrix.hpp> 22 #include <Sequence/VariantMatrixViews.hpp> 24 #include "VariantMatrixFixture.hpp" 25 #include <boost/test/unit_test.hpp> 27 BOOST_FIXTURE_TEST_SUITE(test_classic_stats_with_empty_variant_matrix,
30 BOOST_AUTO_TEST_CASE(test_thetapi)
33 BOOST_REQUIRE_EQUAL(pi, 0.0);
35 BOOST_REQUIRE_EQUAL(pi, 0.0);
38 BOOST_AUTO_TEST_CASE(test_thetaw)
41 BOOST_REQUIRE_EQUAL(tw, 0.0);
43 BOOST_REQUIRE_EQUAL(tw, 0.0);
46 BOOST_AUTO_TEST_CASE(test_thetah)
49 BOOST_REQUIRE_EQUAL(th, 0.0);
51 BOOST_REQUIRE_EQUAL(th, 0.0);
54 BOOST_AUTO_TEST_CASE(test_thetal)
57 BOOST_REQUIRE_EQUAL(tl, 0.0);
59 BOOST_REQUIRE_EQUAL(tl, 0.0);
62 BOOST_AUTO_TEST_CASE(test_tajd)
65 BOOST_REQUIRE_EQUAL(std::isnan(td),
true);
67 BOOST_REQUIRE_EQUAL(std::isnan(td),
true);
70 BOOST_AUTO_TEST_CASE(test_faywuh)
73 BOOST_REQUIRE_EQUAL(std::isnan(fwh),
true);
75 BOOST_REQUIRE_EQUAL(std::isnan(fwh),
true);
78 BOOST_AUTO_TEST_CASE(test_hprime)
81 BOOST_REQUIRE_EQUAL(std::isnan(hp),
true);
83 BOOST_REQUIRE_EQUAL(std::isnan(hp),
true);
90 BOOST_AUTO_TEST_CASE(test_num_haplotypes)
93 BOOST_REQUIRE_EQUAL(nh, -1);
95 BOOST_REQUIRE_EQUAL(nh, 1);
98 BOOST_AUTO_TEST_CASE(test_haplotype_diversity)
101 BOOST_REQUIRE_EQUAL(std::isnan(hd),
true);
103 BOOST_REQUIRE_EQUAL(hd, 0.0);
106 BOOST_AUTO_TEST_CASE(test_rmin)
109 BOOST_CHECK_EQUAL(rm, -1);
111 BOOST_CHECK_EQUAL(rm, 0);
114 BOOST_AUTO_TEST_SUITE_END()
double hprime(const AlleleCountMatrix &ac, const std::int8_t refstate)
double thetal(const AlleleCountMatrix &ac, const std::int8_t refstate)
Zeng et al. .
double thetah(const AlleleCountMatrix &ac, const std::int8_t refstate)
Fay and Wu's .
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.
"Classic" summaries of variation data.
double thetapi(const AlleleCountMatrix &ac)
Mean pairwise differences.
double faywuh(const AlleleCountMatrix &ac, const std::int8_t refstate)
Fay and Wu's H.
double thetaw(const AlleleCountMatrix &ac)
Watterson's theta.
std::int32_t rmin(const VariantMatrix &m)
double haplotype_diversity(const VariantMatrix &m)
Calculate the haplotype diversity of a sample.