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#include <iostream>
#include <seqan/align_parallel.h>
#include <seqan/stream.h> // for printing strings
int main()
{
using TSequence = seqan2::String<seqan2::Dna>;
using TAlignedSequence = seqan2::Gaps<TSequence>;
using TThreadModel = seqan2::Parallel;
using TVectorSpec = seqan2::Vectorial;
using TExecPolicy = seqan2::ExecutionPolicy<TThreadModel, TVectorSpec>;
// dummy sequences
TSequence seqH = "CGATT";
TSequence seqV = "CGAAATT";
seqan2::StringSet<TAlignedSequence> seqs1;
seqan2::StringSet<TAlignedSequence> seqs2;
for (size_t i = 0; i < 100; ++i)
{
appendValue(seqs1, TAlignedSequence(seqH));
appendValue(seqs2, TAlignedSequence(seqV));
}
TExecPolicy execPolicy;
setNumThreads(execPolicy, 4);
seqan2::Score<int16_t, seqan2::Simple> scoreAffine(2, -2, -1, -4);
seqan2::String<int16_t> scores = seqan2::localAlignment(execPolicy, seqs1, seqs2, scoreAffine);
for (int16_t score : scores)
std::cout << "Score: " << score << "\n";
for (size_t pos = 0; pos < seqan2::length(seqs1); ++pos) // print out alignments
{
std::cout << seqs1[pos] << "\n";
std::cout << seqs2[pos] << "\n\n";
}
return EXIT_SUCCESS;
}
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