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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <span>
#include <seqan3/alignment/configuration/all.hpp>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/search/fm_index/fm_index.hpp>
#include <seqan3/search/search.hpp>
using namespace seqan3::literals;
// Define the pairwise alignment configuration globally.
inline constexpr auto align_config =
seqan3::align_cfg::method_global{seqan3::align_cfg::free_end_gaps_sequence1_leading{true},
seqan3::align_cfg::free_end_gaps_sequence2_leading{false},
seqan3::align_cfg::free_end_gaps_sequence1_trailing{true},
seqan3::align_cfg::free_end_gaps_sequence2_trailing{false}}
| seqan3::align_cfg::edit_scheme | seqan3::align_cfg::output_alignment{} | seqan3::align_cfg::output_score{};
void run_text_single()
{
seqan3::dna4_vector text{
"CGCTGTCTGAAGGATGAGTGTCAGCCAGTGTAACCCGATGAGCTACCCAGTAGTCGAACTGGGCCAGACAACCCGGCGCTAATGCACTCA"_dna4};
seqan3::dna4_vector query{"GCT"_dna4};
seqan3::fm_index index{text};
seqan3::debug_stream << "Searching all best hits allowing for 1 error in a single text\n";
seqan3::configuration const search_config =
seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} | seqan3::search_cfg::hit_all_best{};
auto search_results = search(query, index, search_config);
seqan3::debug_stream << "-----------------\n";
for (auto && hit : search_results)
{
size_t start = hit.reference_begin_position() ? hit.reference_begin_position() - 1 : 0;
std::span text_view{std::data(text) + start, query.size() + 1};
for (auto && res : align_pairwise(std::tie(text_view, query), align_config))
{
auto && [aligned_database, aligned_query] = res.alignment();
seqan3::debug_stream << "score: " << res.score() << '\n';
seqan3::debug_stream << "database: " << aligned_database << '\n';
seqan3::debug_stream << "query: " << aligned_query << '\n';
seqan3::debug_stream << "=============\n";
}
}
}
void run_text_collection()
{
std::vector<seqan3::dna4_vector> text{"CGCTGTCTGAAGGATGAGTGTCAGCCAGTGTA"_dna4,
"ACCCGATGAGCTACCCAGTAGTCGAACTG"_dna4,
"GGCCAGACAACCCGGCGCTAATGCACTCA"_dna4};
seqan3::dna4_vector query{"GCT"_dna4};
seqan3::fm_index index{text};
seqan3::debug_stream << "Searching all best hits allowing for 1 error in a text collection\n";
seqan3::configuration const search_config =
seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}} | seqan3::search_cfg::hit_all_best{};
seqan3::debug_stream << "-----------------\n";
for (auto && hit : search(query, index, search_config))
{
size_t start = hit.reference_begin_position() ? hit.reference_begin_position() - 1 : 0;
std::span text_view{std::data(text[hit.reference_id()]) + start, query.size() + 1};
for (auto && res : align_pairwise(std::tie(text_view, query), align_config))
{
auto && [aligned_database, aligned_query] = res.alignment();
seqan3::debug_stream << "score: " << res.score() << '\n';
seqan3::debug_stream << "database: " << aligned_database << '\n';
seqan3::debug_stream << "query: " << aligned_query << '\n';
seqan3::debug_stream << "=============\n";
}
}
}
int main()
{
run_text_single();
seqan3::debug_stream << '\n';
run_text_collection();
}
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