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#include <iostream>
#include <seqan/basic.h>
#include <seqan/align.h>
#include <seqan/sequence.h>
#include <seqan/stream.h> // for printint strings
using namespace seqan;
int main()
{
Dna5String seqH = "CGATT";
Dna5String seqV = "CGAAATT";
Align<Dna5String> align;
resize(rows(align), 2);
assignSource(row(align, 0), seqH);
assignSource(row(align, 1), seqV);
Score<int, Simple> scoringScheme(2, -1, -2);
AlignConfig<> alignConfig;
int lDiag = -2;
int uDiag = 2;
int result = globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag);
std::cout << "Score: " << result << "\n";
std::cout << "The resulting alignment is\n"
<< align << "\n";
return 0;
}
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