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//![Complete]
#include <set>
#include <mutex>
#include <seqan/index.h>
using namespace seqan2;
int main()
{
DnaString genome(
"GAGAGGCCACTCGCAGGATTAAGTCAATAAGTTAATGGCGTGGGGTTATGGTATGGGGGTTCTCGCCCACAGTGACCTCATCGGT"
"GCATTTCCTCATCGTAGGCGGAACGGTAGACACAAGGCATGATGTCAAATCGCGACTCCAATCCCAAGGTCGCAAGCCTATATAG"
"GAACCCGCTTATGCCCTCTAATCCCGGACAGACCCCAAATATGGCATAGCTGGTTGGGGGTACCTACTAGGCACAGCCGGAAGCA");
Index<DnaString, BidirectionalIndex<FMIndex<> > > index(genome);
//![Delegate]
auto delegate = [](auto & iter, DnaString const &, uint8_t /* errors */)
{
for (auto occ : getOccurrences(iter))
std::cout << occ << std::endl;
};
//![Delegate]
DnaString pattern("GGGGTTAT");
std::cout << "Hits with up to 2 errors (HammingDistance):" << std::endl;
//![SinglePattern]
find<0, 2>(delegate, index, pattern, HammingDistance());
//![SinglePattern]
StringSet<DnaString> patterns;
appendValue(patterns, "GGGGTTAT");
appendValue(patterns, "CTAGCTAA");
std::cout << "Hits with 1-2 errors (HammingDistance):" << std::endl;
//![MultiplePatterns]
find<1, 2>(delegate, index, patterns, HammingDistance(), Serial());
//![MultiplePatterns]
//![ParallelMode]
std::mutex mtx;
std::set<Pair<DnaString, unsigned> > hits;
auto delegateParallel = [&hits, &mtx](auto & iter, DnaString const & needle, uint8_t /* errors */)
{
std::lock_guard<std::mutex> lck(mtx); // critical section below this line
for (auto occ : getOccurrences(iter))
hits.insert(Pair<DnaString, unsigned>(needle, occ));
};
find<2, 3>(delegateParallel, index, patterns, HammingDistance(), Parallel());
std::cout << "Hits with 2-3 errors (HammingDistance, no duplicates):" << std::endl;
for (auto hit : hits)
std::cout << hit << std::endl;
//![ParallelMode]
return 0;
}
//![Complete]
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