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|
// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
#include <gtest/gtest.h>
#include <algorithm>
#include <type_traits>
#include <seqan3/range/views/persist.hpp>
#include <seqan3/search/configuration/hit.hpp>
#include <seqan3/search/configuration/max_error.hpp>
#include <seqan3/search/configuration/on_result.hpp>
#include <seqan3/search/fm_index/bi_fm_index.hpp>
#include <seqan3/search/fm_index/fm_index.hpp>
#include <seqan3/search/search.hpp>
#include <seqan3/test/expect_range_eq.hpp>
#include "helper.hpp"
using seqan3::operator""_dna4;
using seqan3::operator""_phred42;
using namespace std::string_literals;
auto position = seqan3::views::persist |
std::views::transform([] (auto && res) { return res.reference_begin_position(); });
auto query_id = seqan3::views::persist | std::views::transform([] (auto && res) { return res.query_id(); });
template <typename index_t>
class search_test : public ::testing::Test
{
public:
seqan3::dna4_vector text{"ACGTACGTACGT"_dna4};
index_t index{text};
};
template <typename index_t>
class search_string_test : public ::testing::Test
{
public:
std::string text{"Garfield the fat cat."};
index_t index{text};
};
using fm_index_types = ::testing::Types<seqan3::fm_index<seqan3::dna4, seqan3::text_layout::single>,
seqan3::bi_fm_index<seqan3::dna4, seqan3::text_layout::single>>;
using fm_index_string_types = ::testing::Types<seqan3::fm_index<char, seqan3::text_layout::single>,
seqan3::bi_fm_index<char, seqan3::text_layout::single>>;
TYPED_TEST_SUITE(search_test, fm_index_types, );
TYPED_TEST_SUITE(search_string_test, fm_index_string_types, );
TYPED_TEST(search_test, error_free)
{
{
// successful and unsuccesful exact search without cfg
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index) | position, (std::vector{0, 4, 8}));
EXPECT_RANGE_EQ(search("ACGG"_dna4, this->index) | position, (std::vector<int>{}));
}
{
// successful and unsuccesful exact search with empty cfg
seqan3::configuration const cfg;
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position, (std::vector{0, 4, 8}));
EXPECT_RANGE_EQ(search("ACGG"_dna4, this->index, cfg) | position, (std::vector<int>{}));
}
{
// successful and unsuccesful exact search using empty error_count
// default max_error_total{error_count{}} sets all error to 0
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{}};
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position, (std::vector{0, 4, 8}));
EXPECT_RANGE_EQ(search("ACGG"_dna4, this->index, cfg) | position, (std::vector<int>{}));
}
{
// successful and unsuccesful exact search using empty error_rate
// default max_error_total{error_rate{}} sets all error to 0.0
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_rate{}};
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position, (std::vector{0, 4, 8}));
EXPECT_RANGE_EQ(search("ACGG"_dna4, this->index, cfg) | position, (std::vector<int>{}));
}
}
TYPED_TEST(search_test, on_result_invocation)
{
std::vector<int> actual_positions{};
seqan3::configuration const cfg = seqan3::search_cfg::on_result{[&] (auto && search_result) -> void
{
actual_positions.push_back(search_result.reference_begin_position());
}};
search("ACGT"_dna4, this->index, cfg);
EXPECT_RANGE_EQ(actual_positions, (std::vector{0, 4, 8}));
actual_positions.clear();
search("ACGG"_dna4, this->index, cfg);
EXPECT_TRUE(actual_positions.empty());
}
TYPED_TEST(search_test, convertible_query)
{
std::vector<seqan3::qualified<seqan3::dna4, seqan3::phred42>> query{{'A'_dna4, '!'_phred42},
{'C'_dna4, '!'_phred42},
{'G'_dna4, '!'_phred42},
{'T'_dna4, '!'_phred42}};
EXPECT_RANGE_EQ(search(query, this->index) | position, (std::vector{0, 4, 8}));
}
TYPED_TEST(search_test, multiple_queries)
{
std::vector<std::vector<seqan3::dna4>> const queries{{"GG"_dna4, "ACGTACGTACGT"_dna4, "ACGTA"_dna4}};
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_rate{.0}} |
seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_rate{.0}} |
seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_rate{.0}} |
seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_rate{.0}};
EXPECT_RANGE_EQ(search(queries, this->index, cfg) | query_id, (std::vector{1, 2, 2}));
EXPECT_RANGE_EQ(search(queries, this->index, cfg) | position, (std::vector{0, 0, 4}));
}
TYPED_TEST(search_test, parallel_queries)
{
constexpr size_t num_queries{100u};
std::vector<std::vector<seqan3::dna4>> const queries{num_queries, {"ACGTACGTACGT"_dna4}};
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_rate{.0}} |
seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_rate{.0}} |
seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_rate{.0}} |
seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_rate{.0}} |
seqan3::search_cfg::parallel{
std::min<uint32_t>(2, std::thread::hardware_concurrency())};
EXPECT_RANGE_EQ(search(queries, this->index, cfg) | query_id, std::views::iota(0u, num_queries));
EXPECT_RANGE_EQ(search(queries, this->index, cfg) | position, std::vector(num_queries, 0));
}
TYPED_TEST(search_test, invalid_error_configuration)
{
seqan3::configuration const cfg1 = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_rate{-0.5}};
EXPECT_THROW(search("A"_dna4, this->index, cfg1).begin(), std::invalid_argument);
seqan3::configuration const cfg2 = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_rate{2.0}};
EXPECT_THROW(search("A"_dna4, this->index, cfg2).begin(), std::invalid_argument);
seqan3::configuration const cfg3 = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{0}} |
seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_count{1}};
EXPECT_THROW(search("A"_dna4, this->index, cfg3).begin(), std::invalid_argument);
seqan3::configuration const cfg4 = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{0}} |
seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_count{1}};
EXPECT_THROW(search("A"_dna4, this->index, cfg4).begin(), std::invalid_argument);
seqan3::configuration const cfg5 = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{0}} |
seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{1}};
EXPECT_THROW(search("A"_dna4, this->index, cfg5).begin(), std::invalid_argument);
}
TYPED_TEST(search_test, invalid_dynamic_hit_configuration)
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit{};
EXPECT_THROW(search("A"_dna4, this->index, cfg), std::invalid_argument);
}
TYPED_TEST(search_test, error_substitution)
{
{
seqan3::configuration const cfg =
seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_rate{.25}};
EXPECT_RANGE_EQ(search("ACGT"_dna4 , this->index, cfg) | position, (std::vector{0, 4, 8})); // exact match
EXPECT_RANGE_EQ(search("CGG"_dna4 , this->index, cfg) | position, (std::vector<int>{})); // not enough mismatches
EXPECT_RANGE_EQ(search("CGTC"_dna4 , this->index, cfg) | position, (std::vector{1, 5})); // 1 mismatch
EXPECT_RANGE_EQ(search("ACGGACG"_dna4 , this->index, cfg) | position, (std::vector{0, 4})); // 1 mismatch
EXPECT_RANGE_EQ(search("ACGGACGG"_dna4, this->index, cfg) | position, (std::vector{0, 4})); // 2 mismatches
}
{
seqan3::configuration const cfg =
seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_count{1}};
EXPECT_RANGE_EQ(search("ACGT"_dna4 , this->index, cfg) | position, (std::vector{0, 4, 8})); // exact match
EXPECT_RANGE_EQ(search("CGTTT"_dna4 , this->index, cfg) | position, (std::vector<int>{})); // not enough mismatches
EXPECT_RANGE_EQ(search("CGG"_dna4 , this->index, cfg) | position, (std::vector{1, 5, 9})); // 1 mismatch
EXPECT_RANGE_EQ(search("ACGGACG"_dna4 , this->index, cfg) | position, (std::vector{0, 4})); // 1 mismatch
EXPECT_RANGE_EQ(search("CGTCCGTA"_dna4, this->index, cfg) | position, (std::vector{1})); // 1 mismatch
}
}
TYPED_TEST(search_test, error_configuration_types)
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_count{1}};
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position, (std::vector{0, 4, 8}));
}
TYPED_TEST(search_test, error_insertion)
{
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_rate{.25}};
// exact match and insertion at the beginning of the query
EXPECT_RANGE_EQ(search("ACGT"_dna4 , this->index, cfg) | position, (std::vector{0, 1, 4, 5, 8, 9}));
// 1 insertion
EXPECT_RANGE_EQ(search("CCGT"_dna4 , this->index, cfg) | position, (std::vector{1, 5, 9}));
// 2 insertions
EXPECT_RANGE_EQ(search("ACCGGTAC"_dna4, this->index, cfg) | position, (std::vector{0, 4}));
// 2 insertions necessary, only 1 allowed
EXPECT_RANGE_EQ(search("ACCGG"_dna4, this->index, cfg) | position, (std::vector<int>{}));
// deletion necessary, not allowed
EXPECT_RANGE_EQ(search("ACTACGT"_dna4, this->index, cfg) | position, (std::vector<int>{}));
}
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_count{1}};
// exact match and insertion at the beginning of the query
EXPECT_RANGE_EQ(search("ACGT"_dna4 , this->index, cfg) | position, (std::vector{0, 1, 4, 5, 8, 9}));
// 1 insertion
EXPECT_RANGE_EQ(search("CCGT"_dna4 , this->index, cfg) | position, (std::vector{1, 5, 9}));
// 2 insertions necessary, only 1 allowed
EXPECT_RANGE_EQ(search("ACCGGTAC"_dna4, this->index, cfg) | position, (std::vector<int>{}));
// deletion necessary, not allowed
EXPECT_RANGE_EQ(search("ACTACGT"_dna4, this->index, cfg) | position, (std::vector<int>{}));
}
}
TYPED_TEST(search_test, error_deletion)
{
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_rate{.25}};
// exact match, no deletion
EXPECT_RANGE_EQ(search("ACGT"_dna4 , this->index, cfg) | position, (std::vector{0, 4, 8}));
// not enough max errors
EXPECT_RANGE_EQ(search("AGT"_dna4, this->index, cfg) | position, (std::vector<int>{}));
// one deletion (C)
EXPECT_RANGE_EQ(search("AGTA"_dna4 , this->index, cfg) | position, (std::vector{0, 4}));
// two deletion (C)
EXPECT_RANGE_EQ(search("AGTAGTAC"_dna4, this->index, cfg) | position, (std::vector{0}));
// no deletion at beginning. 0 and 4 cannot be reported
EXPECT_RANGE_EQ(search("CGTACGT"_dna4 , this->index, cfg) | position, (std::vector{1, 5}));
}
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{1}};
// exact match, no deletion
EXPECT_RANGE_EQ(search("ACGT"_dna4 , this->index, cfg) | position, (std::vector{0, 4, 8}));
// one deletion (C)
EXPECT_RANGE_EQ(search("AGTA"_dna4 , this->index, cfg) | position, (std::vector{0, 4}));
// 2 deletions necessary, only 1 allowed
EXPECT_RANGE_EQ(search("AGTAGTAC"_dna4, this->index, cfg) | position, (std::vector<int>{}));
// no deletion at beginning. 0 and 4 cannot be reported
EXPECT_RANGE_EQ(search("CGTACGT"_dna4 , this->index, cfg) | position, (std::vector{1, 5}));
}
}
TYPED_TEST(search_test, error_levenshtein)
{
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}};
EXPECT_RANGE_EQ(search("CCGT"_dna4, this->index, cfg) | position, (std::vector{0, 1, 4, 5, 8, 9}));
}
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{2}};
EXPECT_RANGE_EQ(search("CCGT"_dna4, this->index, cfg) | position,
(std::vector{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10}));
}
}
TYPED_TEST(search_test, error_indel_no_substitution)
{
{
// Match one mismatch with 1 insertion and deletion since mismatches are not allowed.
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{2}} |
seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_count{2}} |
seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{2}};
EXPECT_RANGE_EQ(search("GTACCTAC"_dna4, this->index, cfg) | position, (std::vector{2}));
}
{
// Enumerate a deletion and match one mismatch with 1 insertion and deletion since mismatches are not allowed.
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{3}} |
seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_count{3}} |
seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{3}};
EXPECT_RANGE_EQ(search("GTATCCTAC"_dna4, this->index, cfg) | position, (std::vector{2}));
}
}
TYPED_TEST(search_test, search_strategy_all)
{
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}};
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position, (std::vector{0, 1, 4, 5, 8, 9}));
}
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_all{};
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position, (std::vector{0, 1, 4, 5, 8, 9}));
}
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit{seqan3::search_cfg::hit_all{}};
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position, (std::vector{0, 1, 4, 5, 8, 9}));
}
}
TYPED_TEST(search_test, search_strategy_best)
{
std::vector possible_hits{0, 4, 8}; // any of 0, 4, 8 ... 1, 5, 9 are not best hits
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_single_best{};
std::vector result = search("ACGT"_dna4, this->index, cfg) | position | seqan3::views::to<std::vector>;
ASSERT_EQ(result.size(), 1u);
EXPECT_TRUE(std::find(possible_hits.begin(), possible_hits.end(), result[0]) != possible_hits.end());
EXPECT_RANGE_EQ(search("AAAA"_dna4, this->index, cfg) | position, (std::vector<int>{})); // no hit
}
{ // Find best match with 1 insertion at the end.
seqan3::configuration const cfg = seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_single_best{};
std::vector result = search("ACGTT"_dna4, this->index, cfg) | position | seqan3::views::to<std::vector>;
ASSERT_EQ(result.size(), 1u);
EXPECT_TRUE(std::find(possible_hits.begin(), possible_hits.end(), result[0]) != possible_hits.end());
}
{ // Find best match with a match at the end, allowing a insertion.
seqan3::configuration const cfg = seqan3::search_cfg::max_error_insertion{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_single_best{};
std::vector result = search("ACGT"_dna4, this->index, cfg) | position | seqan3::views::to<std::vector>;
ASSERT_EQ(result.size(), 1u);
EXPECT_TRUE(std::find(possible_hits.begin(), possible_hits.end(), result[0]) != possible_hits.end());
}
{ // Find best match with a deletion.
seqan3::configuration const cfg = seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_single_best{};
std::vector result = search("AGT"_dna4, this->index, cfg) | position | seqan3::views::to<std::vector>;
ASSERT_EQ(result.size(), 1u);
EXPECT_TRUE(std::find(possible_hits.begin(), possible_hits.end(), result[0]) != possible_hits.end());
}
{ // Find best match with a match at the end, allowing a deletion.
seqan3::configuration const cfg = seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_single_best{};
std::vector result = search("ACGT"_dna4, this->index, cfg) | position | seqan3::views::to<std::vector>;
ASSERT_EQ(result.size(), 1u);
EXPECT_TRUE(std::find(possible_hits.begin(), possible_hits.end(), result[0]) != possible_hits.end());
}
{ // Find best match with a substitution at the end.
seqan3::configuration const cfg =
seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_single_best{};
std::vector result = search("ACGC"_dna4, this->index, cfg) | position | seqan3::views::to<std::vector>;
ASSERT_EQ(result.size(), 1u);
EXPECT_TRUE(std::find(possible_hits.begin(), possible_hits.end(), result[0]) != possible_hits.end());
}
{ // Find best match with a match at the end, allowing a substitution.
seqan3::configuration const cfg =
seqan3::search_cfg::max_error_substitution{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_single_best{};
std::vector result = search("ACGT"_dna4, this->index, cfg) | position | seqan3::views::to<std::vector>;
ASSERT_EQ(result.size(), 1u);
EXPECT_TRUE(std::find(possible_hits.begin(), possible_hits.end(), result[0]) != possible_hits.end());
}
{ // Find best match with 2 deletions.
std::vector possible_hits2d{0, 4}; // any of 0, 4 ... 1, 5 are not best hits
seqan3::configuration const cfg = seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{2}} |
seqan3::search_cfg::hit_single_best{};
std::vector result = search("AGTAGT"_dna4, this->index, cfg) | position | seqan3::views::to<std::vector>;
ASSERT_EQ(result.size(), 1u);
EXPECT_TRUE(std::find(possible_hits2d.begin(), possible_hits2d.end(), result[0]) != possible_hits2d.end());
}
{ // Find best match with 2 deletions.
std::vector possible_hits2d{0, 4}; // any of 0, 4 ... 1, 5 are not best hits
seqan3::configuration const cfg = seqan3::search_cfg::max_error_deletion{seqan3::search_cfg::error_count{2}} |
seqan3::search_cfg::hit{seqan3::search_cfg::hit_single_best{}};
std::vector result = search("AGTAGT"_dna4, this->index, cfg) | position | seqan3::views::to<std::vector>;
ASSERT_EQ(result.size(), 1u);
EXPECT_TRUE(std::find(possible_hits2d.begin(), possible_hits2d.end(), result[0]) != possible_hits2d.end());
}
}
TYPED_TEST(search_test, search_strategy_all_best)
{
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_all_best{};
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position,
(std::vector{0, 4, 8})); // 1, 5, 9 are not best hits
EXPECT_RANGE_EQ(search("AAAA"_dna4, this->index, cfg) | position, (std::vector<int>{})); // no hit
}
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit{seqan3::search_cfg::hit_all_best{}};
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position,
(std::vector{0, 4, 8})); // 1, 5, 9 are not best hits
EXPECT_RANGE_EQ(search("AAAA"_dna4, this->index, cfg) | position, (std::vector<int>{})); // no hit
}
}
TYPED_TEST(search_test, search_strategy_strata)
{
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_strata{0};
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position, (std::vector{0, 4, 8}));
}
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_strata{1};
EXPECT_RANGE_EQ(search("ACGT"_dna4, this->index, cfg) | position, (std::vector{0, 1, 4, 5, 8, 9}));
}
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit_strata{1};
EXPECT_RANGE_EQ(search("AAAA"_dna4, this->index, cfg) | position, (std::vector<int>{})); // no hit
}
{
seqan3::configuration const cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} |
seqan3::search_cfg::hit{seqan3::search_cfg::hit_strata{1}};
EXPECT_RANGE_EQ(search("AAAA"_dna4, this->index, cfg) | position, (std::vector<int>{})); // no hit
}
// {
// // best hit ACGT with 1 error, i.e. 1+1
// seqan3::configuration const cfg = seqan3::search_cfg::max_total_error{1} |
// seqan3::search_cfg::hit_strata{1};
// EXPECT_RANGE_EQ(search(this->index, "CCGT"_dna4, cfg) | position, (std::vector{0, 1, 2, 3,4, 5, 6, 7,
// 8, 9, 1, 0}));
// }
// {
// // best hit ACGT with 1 error, i.e. 1+1
// seqan3::configuration const cfg = seqan3::search_cfg::max_total_error{1} |
// seqan3::search_cfg::hit_strata{1};
// EXPECT_RANGE_EQ(search(this->index, "CCGT"_dna4, cfg) | position, (std::vector{0, 1, 2, 3, 4, 5, 6, 7,
// 8, 9, 1, 0}));
// }
}
TYPED_TEST(search_test, parallel_without_parameter)
{
seqan3::configuration cfg = seqan3::search_cfg::parallel{};
EXPECT_THROW(search("AAAA"_dna4, this->index, cfg), std::runtime_error);
}
TYPED_TEST(search_string_test, error_free_string)
{
// successful and unsuccesful exact search without cfg
EXPECT_RANGE_EQ(search("at"s, this->index) | position, (std::vector{14, 18}));
EXPECT_RANGE_EQ(search("Jon"s, this->index) | position, (std::vector<int>{}));
}
TYPED_TEST(search_string_test, error_free_raw)
{
// successful and unsuccesful exact search without cfg
EXPECT_RANGE_EQ(search("at", this->index) | position, (std::vector{14, 18}));
EXPECT_RANGE_EQ(search("Jon", this->index) | position, (std::vector<int>{}));
}
TYPED_TEST(search_string_test, multiple_queries_string)
{
std::vector<std::string> const queries{"at", "Jon"};
EXPECT_RANGE_EQ(search(queries, this->index) | position, (std::vector{14, 18})); // 2 and 0 hits
}
TYPED_TEST(search_string_test, multiple_queries_raw)
{
EXPECT_RANGE_EQ(search({"at", "Jon"}, this->index) | position, (std::vector{14, 18})); // 2 and 0 hits
}
// TYPED_TEST(search_test, return_iterator_index)
// {
// }
//
// TYPED_TEST(search_test, on_hit)
// {
// }
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