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#include <seqan/sequence.h>
#include <seqan/stream.h>
#include <seqan/score.h>
#include <seqan/seeds.h>
using namespace seqan;
int main()
{
// The horizontal and vertical sequence (subject and query sequences).
CharString seqH = "The quick BROWN fox jumped again!";
CharString seqV = "thick BROWN boxes of brownies!";
// Create and print the seed sequence.
Seed<Simple> seed(11, 7, 14, 10);
std::cout << "original\n"
<< "seedH: " << infix(seqH, beginPositionH(seed),
endPositionH(seed)) << "\n"
<< "seedV: " << infix(seqV, beginPositionV(seed),
endPositionV(seed)) << "\n";
// Perform match extension.
Score<int, Simple> scoringScheme(1, -1, -1);
extendSeed(seed, seqH, seqV, EXTEND_BOTH, scoringScheme, 3,
GappedXDrop());
// Print the resulting seed.
std::cout << "result\n"
<< "seedH: " << infix(seqH, beginPositionH(seed),
endPositionH(seed)) << "\n"
<< "seedV: " << infix(seqV, beginPositionV(seed),
endPositionV(seed)) << "\n";
return 0;
}
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