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#include "btllib/indexlr.hpp"
#include "btllib/bloom_filter.hpp"
#include "btllib/util.hpp"
#include "helpers.hpp"
#include <fstream>
#include <sstream>
int
main()
{
std::cerr << "Testing on empty file" << std::endl;
btllib::Indexlr indexlr_empty(btllib::get_dirname(__FILE__) + "/empty.fa",
20,
50,
btllib::Indexlr::Flag::LONG_MODE);
int i = 0;
for (auto minimizers : indexlr_empty) {
i++;
}
TEST_ASSERT_EQ(i, 0);
std::cerr << "Testing without Bloom filters" << std::endl;
btllib::Indexlr indexlr(btllib::get_dirname(__FILE__) + "/indexlr.fa",
100,
5,
btllib::Indexlr::Flag::SHORT_MODE);
btllib::Indexlr indexlr2(btllib::get_dirname(__FILE__) + "/indexlr.fq",
100,
5,
btllib::Indexlr::Flag::BX |
btllib::Indexlr::Flag::SEQ |
btllib::Indexlr::Flag::SHORT_MODE);
std::ifstream correct_output_file(btllib::get_dirname(__FILE__) +
"/indexlr.fa.correct");
std::string correct_output;
correct_output_file.seekg(0, std::ios::end);
correct_output.reserve(correct_output_file.tellg());
correct_output_file.seekg(0, std::ios::beg);
correct_output.assign(std::istreambuf_iterator<char>(correct_output_file),
std::istreambuf_iterator<char>());
std::ifstream correct_output_file2(btllib::get_dirname(__FILE__) +
"/indexlr.fq.correct");
std::string correct_output2;
correct_output_file2.seekg(0, std::ios::end);
correct_output2.reserve(correct_output_file2.tellg());
correct_output_file2.seekg(0, std::ios::beg);
correct_output2.assign(std::istreambuf_iterator<char>(correct_output_file2),
std::istreambuf_iterator<char>());
std::stringstream ss;
std::stringstream ss2;
decltype(indexlr)::Record record;
bool success_indexlr = false, success_indexlr2 = false;
for (int i = 0;; i++) {
if ((success_indexlr = (record = indexlr.read()))) {
if (i > 0) {
ss << '\n';
}
ss << record.id << '\t';
int j = 0;
for (const auto& min : record.minimizers) {
if (j > 0) {
ss << ' ';
}
ss << min.out_hash;
j++;
}
}
if ((success_indexlr2 = (record = indexlr2.read()))) {
if (i > 0) {
ss2 << '\n';
}
ss2 << record.id << '\t' << record.barcode << '\t';
int j = 0;
for (const auto& min : record.minimizers) {
if (j > 0) {
ss2 << ' ';
}
ss2 << min.out_hash << ':' << min.pos << ':'
<< (min.forward ? '+' : '-') << ':' << min.seq;
j++;
}
}
if (!success_indexlr && !success_indexlr2) {
break;
}
}
ss << std::endl;
ss2 << std::endl;
TEST_ASSERT_EQ(ss.str(), correct_output);
TEST_ASSERT_EQ(ss2.str(), correct_output2);
std::cerr << "Testing with Bloom filters" << std::endl;
btllib::BloomFilter filter_in_bf(1024 * 1024 * 32, 1);
btllib::BloomFilter filter_out_bf(1024 * 1024 * 32, 1);
std::vector<uint64_t> filter_in_hashes = { 1315163655624994337ULL,
4261937130627716230ULL,
6055236352205909654ULL };
std::vector<uint64_t> filter_out_hashes = { 54854220342742384ULL,
10545593919277017579ULL,
6459583435485319281ULL };
for (const auto h : filter_in_hashes) {
filter_in_bf.insert({ h });
}
for (const auto h : filter_out_hashes) {
filter_out_bf.insert({ h });
}
btllib::Indexlr indexlr3(btllib::get_dirname(__FILE__) + "/indexlr.fq",
100,
5,
btllib::Indexlr::Flag::FILTER_IN |
btllib::Indexlr::Flag::LONG_MODE,
3,
true,
filter_in_bf);
size_t mins_found = 0;
while ((record = indexlr3.read())) {
for (const auto& min : record.minimizers) {
bool found = false;
for (const auto h : filter_in_hashes) {
if (min.min_hash == h) {
found = true;
break;
}
}
TEST_ASSERT(found);
mins_found++;
}
}
TEST_ASSERT_GE(mins_found, filter_in_hashes.size());
btllib::Indexlr indexlr4(btllib::get_dirname(__FILE__) + "/indexlr.fq",
100,
5,
btllib::Indexlr::Flag::FILTER_OUT |
btllib::Indexlr::Flag::LONG_MODE,
3,
true,
filter_out_bf);
mins_found = 0;
while ((record = indexlr4.read())) {
for (const auto& min : record.minimizers) {
for (const auto h : filter_out_hashes) {
TEST_ASSERT_NE(min.min_hash, h);
}
mins_found++;
}
}
TEST_ASSERT_GE(mins_found, filter_in_hashes.size());
btllib::Indexlr indexlr5(btllib::get_dirname(__FILE__) + "/indexlr.fq",
100,
5,
btllib::Indexlr::Flag::FILTER_IN |
btllib::Indexlr::Flag::FILTER_OUT |
btllib::Indexlr::Flag::SHORT_MODE,
3,
true,
filter_in_bf,
filter_out_bf);
mins_found = 0;
while ((record = indexlr5.read())) {
for (const auto& min : record.minimizers) {
bool found = false;
for (const auto h : filter_in_hashes) {
if (min.min_hash == h) {
found = true;
break;
}
}
TEST_ASSERT(found);
for (const auto h : filter_out_hashes) {
TEST_ASSERT_NE(min.min_hash, h);
}
mins_found++;
}
}
TEST_ASSERT_GE(mins_found, filter_in_hashes.size());
return 0;
}
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