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#include <seqan3/alignment/configuration/align_config_method.hpp>
#include <seqan3/alignment/configuration/align_config_scoring_scheme.hpp>
#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 namespace seqan3::literals;
int main()
{
// configure a global alignment for DNA sequences
auto min_cfg = seqan3::align_cfg::method_global{}
| seqan3::align_cfg::scoring_scheme{
seqan3::nucleotide_scoring_scheme{seqan3::match_score{4}, seqan3::mismatch_score{-5}}};
auto seq1 = "TCGT"_dna4;
auto seq2 = "ACGA"_dna4;
for (auto res : seqan3::align_pairwise(std::tie(seq1, seq2), min_cfg))
seqan3::debug_stream << res.score() << '\n'; // print out the alignment score
}
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