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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 <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>
int main()
{
using namespace seqan3::literals;
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.
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
| seqan3::align_cfg::band_fixed_size{seqan3::align_cfg::lower_diagonal{-3},
seqan3::align_cfg::upper_diagonal{8}};
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';
}
}
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