Skip to content

Commit

Permalink
Add more tests
Browse files Browse the repository at this point in the history
  • Loading branch information
@robomics
robomics committed Sep 24, 2023
1 parent 60a50f7 commit a138acd
Show file tree
Hide file tree
Showing 2 changed files with 186 additions and 78 deletions.
2 changes: 1 addition & 1 deletion test/units/balancing/CMakeLists.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ target_sources(hictk_balancing_tests PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/balanci
target_link_libraries(
hictk_balancing_tests
PRIVATE hictk_project_warnings hictk_project_options
PUBLIC hictk::balancing hictk::hic hictk::cooler)
PUBLIC hictk::balancing hictk::file)

target_link_system_libraries(
hictk_balancing_tests
Expand Down
262 changes: 185 additions & 77 deletions test/units/balancing/balancing_test.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,7 @@

#include "hictk/balancing/ice.hpp"
#include "hictk/balancing/methods.hpp"
#include "hictk/balancing/vc.hpp"
#include "hictk/cooler.hpp"
#include "hictk/hic.hpp"
#include "hictk/file.hpp"
#include "tmpdir.hpp"

namespace hictk::test {
Expand Down Expand Up @@ -47,116 +45,226 @@ static void compare_weights(const std::vector<double>& weights, const std::vecto
}
}

template <typename T>
static void compare_vectors(const std::vector<T>& v1, const std::vector<T>& v2) {
REQUIRE(v1.size() == v2.size());

for (std::size_t i = 0; i < v1.size(); ++i) {
CHECK(v1[i] == v2[i]);
}
}

// NOLINTNEXTLINE(readability-function-cognitive-complexity)
TEST_CASE("Balancing: VC", "[balancing][short]") {
const auto path = datadir / "hic/ENCFF993FGR.hic";
TEST_CASE("Balancing: SparseMatrix") {
using SparseMatrix = hictk::balancing::SparseMatrix;
const BinTable bins{Reference{Chromosome{0, "chr0", 50}, Chromosome{1, "chr1", 100},
Chromosome{2, "chr2", 50}, Chromosome{3, "chr3", 50}},
50};
// clang-format off
const std::vector<ThinPixel<std::int32_t>> pixels{
{1, 0, 1}, {1, 1, 2}, {2, 1, 3}, // chr1
{3, 0, 4}, {3, 1, 5}}; // chr2
// clang-format on

SECTION("accessors") {
CHECK(SparseMatrix{}.empty());
CHECK(SparseMatrix{bins}.empty());
}

SECTION("push_back") {
SparseMatrix m{bins};
for (const auto& p : pixels) {
m.push_back(p.bin1_id, p.bin2_id, p.count);
}
m.finalize();
CHECK(m.size() == pixels.size());

m.clear();
CHECK(m.empty());
}

SECTION("subset") {
SparseMatrix m{bins};
for (const auto& p : pixels) {
m.push_back(p.bin1_id, p.bin2_id, p.count);
}
m.finalize();

CHECK(m.subset(0).empty());
CHECK(m.subset(1).size() == 3);
CHECK(m.subset(2).size() == 2);
CHECK(m.subset(3).empty());
}

auto hf = hictk::hic::File(path.string(), 2500000);
SECTION("serde") {
const auto tmpfile = testdir() / "sparse_matrix_serde.bin";

SECTION("empty matrix") {
std::fstream f{};
f.open(tmpfile, std::ios::in | std::ios::out | std::ios::trunc);
f.exceptions(std::ios::badbit | std::ios::failbit);

SparseMatrix m1{};
SparseMatrix m2{};
m1.finalize();
m1.serialize(f);
f.seekg(std::ios::beg);
m2.deserialize(f);

compare_vectors(m1.bin1_ids(), m2.bin1_ids());
compare_vectors(m1.bin2_ids(), m2.bin2_ids());
compare_vectors(m1.counts(), m2.counts());
compare_vectors(m1.chrom_offsets(), m2.chrom_offsets());
}

SECTION("INTRA") {
for (const auto& chrom : hf.chromosomes()) {
if (chrom.is_all()) {
continue;
SECTION("full matrix") {
SparseMatrix m1{bins};
for (const auto& p : pixels) {
m1.push_back(p.bin1_id, p.bin2_id, p.count);
}
auto sel1 = hf.fetch(chrom.name());
m1.finalize();

const auto num_bins = hf.bins().subset(chrom).size();
const auto bin_id_offset = hf.bins().at(chrom.name(), 0).id();
const auto weights =
hictk::balancing::VC<std::int32_t>(sel1.begin<std::int32_t>(), sel1.end<std::int32_t>(),
num_bins, bin_id_offset)
.get_weights();
std::fstream f{};
f.open(tmpfile, std::ios::in | std::ios::out | std::ios::trunc);
f.exceptions(std::ios::badbit | std::ios::failbit);

auto sel2 = hf.fetch(chrom.name(), hictk::balancing::Method::VC());
compare_weights(weights, sel2.weights1()());
SparseMatrix m2{bins};
m1.serialize(f);
f.seekg(std::ios::beg);
m2.deserialize(f);

compare_vectors(m1.bin1_ids(), m2.bin1_ids());
compare_vectors(m1.bin2_ids(), m2.bin2_ids());
compare_vectors(m1.counts(), m2.counts());
compare_vectors(m1.chrom_offsets(), m2.chrom_offsets());
}
}
}

SECTION("GW") {
const auto num_bins = hf.bins().size();
auto sel = hf.fetch();
const auto weights = hictk::balancing::VC<std::int32_t>(sel.begin<std::int32_t>(),
sel.end<std::int32_t>(), num_bins)
.get_weights();
// NOLINTNEXTLINE(readability-function-cognitive-complexity)
TEST_CASE("Balancing: SparseMatrixChunked") {
using SparseMatrixChunked = hictk::balancing::SparseMatrixChunked;
const BinTable bins{Reference{Chromosome{0, "chr0", 50}, Chromosome{1, "chr1", 100},
Chromosome{2, "chr2", 50}, Chromosome{3, "chr3", 50}},
50};
// clang-format off
const std::vector<ThinPixel<std::int32_t>> pixels{
{1, 0, 1}, {1, 1, 2}, {2, 1, 3}, // chr1
{3, 0, 4}, {3, 1, 5}}; // chr2
// clang-format on
const auto tmpfile = testdir() / "sparse_matrix_chunked.tmp";

SECTION("accessors") { CHECK(SparseMatrixChunked{bins, tmpfile, 2, 0}.empty()); }

SECTION("push_back") {
SparseMatrixChunked m{bins, tmpfile, 2, 0};
for (const auto& p : pixels) {
m.push_back(p.bin1_id, p.bin2_id, p.count);
}
m.finalize();

CHECK(m.size() == pixels.size());
}

const auto expected = hf.fetch(hictk::balancing::Method::GW_VC()).weights();
compare_weights(weights, expected);
SECTION("subset") {
SparseMatrixChunked m{bins, tmpfile, 2, 0};
for (const auto& p : pixels) {
m.push_back(p.bin1_id, p.bin2_id, p.count);
}
m.finalize();

CHECK(m.subset(0).empty());
CHECK(m.subset(1).size() == 3);
CHECK(m.subset(2).size() == 2);
CHECK(m.subset(3).empty());
}
}

// NOLINTNEXTLINE(readability-function-cognitive-complexity)
TEST_CASE("Balancing: ICE", "[balancing][long]") {
const auto path = datadir / "cooler/ENCFF993FGR.2500000.cool";
const std::array<std::pair<std::string, std::filesystem::path>, 2> files{
std::make_pair("cooler", datadir / "cooler/ENCFF993FGR.2500000.cool"),
std::make_pair("hic", datadir / "hic/ENCFF993FGR.hic")};

const auto tmpfile = testdir() / "balancing_ice.tmp";

auto clr = hictk::cooler::File(path.string());
for (const auto& [label, path] : files) {
SECTION(label) {
const hictk::File f(path.string(), 2'500'000);

SECTION("in-memory") {
SECTION("INTRA") {
const auto path_intra_weights = datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.cis.txt";
SECTION("in-memory") {
SECTION("INTRA") {
const auto path_intra_weights =
datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.cis.txt";

constexpr auto type = hictk::balancing::ICE::Type::cis;
const auto weights = hictk::balancing::ICE(clr, type).get_weights();
const auto expected_weights = read_weights(path_intra_weights);
constexpr auto type = hictk::balancing::ICE::Type::cis;
const auto weights = hictk::balancing::ICE(f, type).get_weights();
const auto expected_weights = read_weights(path_intra_weights);

compare_weights(weights, expected_weights);
}
compare_weights(weights, expected_weights);
}

SECTION("INTER") {
const auto path_intra_weights =
datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.trans.txt";
SECTION("INTER") {
const auto path_intra_weights =
datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.trans.txt";

constexpr auto type = hictk::balancing::ICE::Type::trans;
const auto weights = hictk::balancing::ICE(clr, type).get_weights();
const auto expected_weights = read_weights(path_intra_weights);
constexpr auto type = hictk::balancing::ICE::Type::trans;
const auto weights = hictk::balancing::ICE(f, type).get_weights();
const auto expected_weights = read_weights(path_intra_weights);

compare_weights(weights, expected_weights);
}
compare_weights(weights, expected_weights);
}

SECTION("GW") {
const auto path_intra_weights = datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.gw.txt";
SECTION("GW") {
const auto path_intra_weights =
datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.gw.txt";

constexpr auto type = hictk::balancing::ICE::Type::gw;
const auto weights = hictk::balancing::ICE(clr, type).get_weights();
const auto expected_weights = read_weights(path_intra_weights);
constexpr auto type = hictk::balancing::ICE::Type::gw;
const auto weights = hictk::balancing::ICE(f, type).get_weights();
const auto expected_weights = read_weights(path_intra_weights);

compare_weights(weights, expected_weights);
}
}
compare_weights(weights, expected_weights);
}
}

SECTION("chunked") {
auto params = hictk::balancing::ICE::DefaultParams;
params.tmpfile = tmpfile;
SECTION("chunked") {
auto params = hictk::balancing::ICE::DefaultParams;
params.tmpfile = tmpfile;
params.chunk_size = 1000;

SECTION("INTRA") {
const auto path_intra_weights = datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.cis.txt";
SECTION("INTRA") {
const auto path_intra_weights =
datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.cis.txt";

constexpr auto type = hictk::balancing::ICE::Type::cis;
const auto weights = hictk::balancing::ICE(clr, type, params).get_weights();
const auto expected_weights = read_weights(path_intra_weights);
constexpr auto type = hictk::balancing::ICE::Type::cis;
const auto weights = hictk::balancing::ICE(f, type, params).get_weights();
const auto expected_weights = read_weights(path_intra_weights);

compare_weights(weights, expected_weights);
}
compare_weights(weights, expected_weights);
}

SECTION("INTER") {
const auto path_intra_weights =
datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.trans.txt";
SECTION("INTER") {
const auto path_intra_weights =
datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.trans.txt";

constexpr auto type = hictk::balancing::ICE::Type::trans;
const auto weights = hictk::balancing::ICE(clr, type, params).get_weights();
const auto expected_weights = read_weights(path_intra_weights);
constexpr auto type = hictk::balancing::ICE::Type::trans;
const auto weights = hictk::balancing::ICE(f, type, params).get_weights();
const auto expected_weights = read_weights(path_intra_weights);

compare_weights(weights, expected_weights);
}
compare_weights(weights, expected_weights);
}

SECTION("GW") {
const auto path_intra_weights = datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.gw.txt";
SECTION("GW") {
const auto path_intra_weights =
datadir / "cooler/balancing/ENCFF993FGR.2500000.ICE.gw.txt";

constexpr auto type = hictk::balancing::ICE::Type::gw;
const auto weights = hictk::balancing::ICE(clr, type, params).get_weights();
const auto expected_weights = read_weights(path_intra_weights);
constexpr auto type = hictk::balancing::ICE::Type::gw;
const auto weights = hictk::balancing::ICE(f, type, params).get_weights();
const auto expected_weights = read_weights(path_intra_weights);

compare_weights(weights, expected_weights);
compare_weights(weights, expected_weights);
}
}
}
}
}
Expand Down

0 comments on commit a138acd

Please sign in to comment.