#include <utility>

#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>

using seqan3::operator""_dna4;

int main()
{
    auto seq1 = "TTACGTACGGACTAGCTACAACATTACGGACTAC"_dna4;
    auto seq2 = "GGACGACATGACGTACGACTTTACGTACGACTAGC"_dna4;

    // Configure the output:
    auto output_config = seqan3::align_cfg::output_score{} |
                         seqan3::align_cfg::output_begin_position{} |
                         seqan3::align_cfg::output_end_position{} |
                         seqan3::align_cfg::output_alignment{};

    // Configure the alignment kernel together with the previous output configuration.
    auto config = seqan3::align_cfg::method_global{
                      seqan3::align_cfg::free_end_gaps_sequence1_leading{true},
                      seqan3::align_cfg::free_end_gaps_sequence2_leading{true},
                      seqan3::align_cfg::free_end_gaps_sequence1_trailing{true},
                      seqan3::align_cfg::free_end_gaps_sequence2_trailing{true}} |
                  seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{
                      seqan3::match_score{4}, seqan3::mismatch_score{-2}}} |
                  seqan3::align_cfg::gap_cost_affine{seqan3::align_cfg::open_score{0},
                                                     seqan3::align_cfg::extension_score{-4}} |
                  output_config;

    for (auto const & res : seqan3::align_pairwise(std::tie(seq1, seq2), config))
    {
        seqan3::debug_stream << "Score: " << res.score() << '\n';
        seqan3::debug_stream << "Begin: (" << res.sequence1_begin_position() << "," << res.sequence2_begin_position()
                             << ")\n";
        seqan3::debug_stream << "End: (" << res.sequence1_end_position() << "," << res.sequence2_end_position()
                             << ")\n";
        seqan3::debug_stream << "Alignment: \n" << res.alignment() << '\n';
    }
}
