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#include <seqan/sequence.h>
#include <seqan/align.h>
#include <seqan/score.h>
#include <seqan/seeds.h>
using namespace seqan;
int main()
{
typedef Seed<Simple> TSeed;
Dna5String sequenceH = "CGAATCCATCCCACACA";
Dna5String sequenceV = "GGCGATNNNCATGGCACA";
Score<int, Simple> scoringSchemeAnchor(0, -1, -1);
Score<int, Simple> scoringSchemeGap(2, -1, -1, -2);
String<TSeed> seedChain;
appendValue(seedChain, TSeed(0, 2, 5, 6));
appendValue(seedChain, TSeed(6, 9, 9, 12));
appendValue(seedChain, TSeed(11, 14, 17, 16));
Align<Dna5String, ArrayGaps> alignment;
resize(rows(alignment), 2);
assignSource(row(alignment, 0), sequenceH);
assignSource(row(alignment, 1), sequenceV);
AlignConfig<true, false, false, true> alignConfig;
int result = bandedChainAlignment(alignment, seedChain, scoringSchemeAnchor, scoringSchemeGap, alignConfig, 2);
std::cout << "Score: " << result << std::endl;
std::cout << alignment << std::endl;
return 0;
}
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