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#include <vector>
#include <seqan3/alignment/configuration/align_config_edit.hpp>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
int main()
{
using namespace seqan3::literals;
// Basic alignment algorithm configuration.
auto config = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme;
std::pair p{"ACGTAGC"_dna4, "AGTACGACG"_dna4};
// Compute only the score:
for (auto res : seqan3::align_pairwise(p, config | seqan3::align_cfg::output_score{}))
seqan3::debug_stream << res << "\n"; // prints: {score: -4}
// Compute only the alignment:
for (auto res : seqan3::align_pairwise(p, config | seqan3::align_cfg::output_alignment{}))
seqan3::debug_stream << res << "\n"; // prints: {alignment: (ACGTA-G-C-,A-GTACGACG)}
// Compute the score and the alignment:
for (auto res :
seqan3::align_pairwise(p, config | seqan3::align_cfg::output_score{} | seqan3::align_cfg::output_alignment{}))
seqan3::debug_stream << res << "\n"; // prints: {score: -4, alignment: (ACGTA-G-C-,A-GTACGACG)}
// By default compute everything:
for (auto res : seqan3::align_pairwise(p, config))
seqan3::debug_stream
<< res << "\n"; // prints {id: 0, score: -4, begin: (0,0), end: (7,9) alignment: (ACGTA-G-C-,A-GTACGACG)}
}
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