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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 <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/search/fm_index/fm_index.hpp>
#include <seqan3/search/search.hpp>
int main()
{
using namespace seqan3::literals;
seqan3::dna4_vector text{
"CGCTGTCTGAAGGATGAGTGTCAGCCAGTGTAACCCGATGAGCTACCCAGTAGTCGAACTGGGCCAGACAACCCGGCGCTAATGCACTCA"_dna4};
seqan3::dna4_vector query{"GCT"_dna4};
seqan3::fm_index index{text};
seqan3::debug_stream << "Searching all hits\n";
seqan3::configuration cfg = seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{1}}
| seqan3::search_cfg::hit{seqan3::search_cfg::hit_all{}};
auto results_all = search(query, index, cfg);
// Attention: results_all is a pure std::ranges::input_range,
// so after calling std::ranges::distance, you cannot iterate over it again!
seqan3::debug_stream << "There are " << std::ranges::distance(results_all) << " hits.\n";
seqan3::debug_stream << "Searching all best hits\n";
using seqan3::get;
get<seqan3::search_cfg::hit>(cfg).hit_variant = seqan3::search_cfg::hit_all_best{};
auto results_all_best = search(query, index, cfg);
// Attention: results_all_best is a pure std::ranges::input_range,
// so after calling std::ranges::distance, you cannot iterate over it again!
seqan3::debug_stream << "There are " << std::ranges::distance(results_all_best) << " hits.\n";
seqan3::debug_stream << "Searching best hit\n";
get<seqan3::search_cfg::hit>(cfg).hit_variant = seqan3::search_cfg::hit_single_best{};
auto results_best = search(query, index, cfg);
// Attention: results_best is a pure std::ranges::input_range,
// so after calling std::ranges::distance, you cannot iterate over it again!
seqan3::debug_stream << "There is " << std::ranges::distance(results_best) << " hits.\n";
seqan3::debug_stream << "Searching all hits in the 1-stratum\n";
get<seqan3::search_cfg::hit>(cfg).hit_variant = seqan3::search_cfg::hit_strata{1};
auto results_strata = search(query, index, cfg);
// Attention: results_strata is a pure std::ranges::input_range,
// so after calling std::ranges::distance, you cannot iterate over it again!
seqan3::debug_stream << "There are " << std::ranges::distance(results_strata) << " hits.\n";
}
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