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#include <seqan/align.h>
#include <seqan/basic.h>
#include <seqan/stream.h> // for printing Seqan strings
using namespace seqan;
int main()
{
Dna5String seq = "CGGTATC";
// Construct the gaps object.
Gaps<Dna5String> gaps(seq);
// Insert gaps (view position, unclipped as of yet). Note that inserting
// the gaps changes the coordinates.
insertGap(gaps, 3);
insertGap(gaps, 5);
insertGaps(gaps, 7, 2);
// Clip the gaps object. Note that the coordinates are in unclipped view position.
setClippedBeginPosition(gaps, 1);
setClippedEndPosition(gaps, 8);
// Print the resulting gaps object and some coordinate transformation.
std::cout << "Resulting gaps: " << gaps << "\n"
<< "toSourcePosition(gaps, 0) == " << toSourcePosition(gaps, 0) << "\n"
<< "toSourcePosition(gaps, 4) == " << toSourcePosition(gaps, 4) << "\n"
<< "toViewPosition(gaps, 0) == " << toViewPosition(gaps, 0) << "\n"
<< "toViewPosition(gaps, 5) == " << toViewPosition(gaps, 6) << "\n";
return 0;
}
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