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#include <seqan/sequence.h>
#include <seqan/index.h>
using namespace seqan;
int main()
{
DnaString genome = "ACGACGTGCAACGTACGACTAGCATCGGATCAGCAT";
Shape<Dna, OneGappedShape> myShape;
stringToShape(myShape, "1101");
// compute hash of a search pattern
unsigned hashedPattern = hash(myShape, "ACGA");
std::cout << "The hash is: " << hashedPattern << std::endl;
// compute all overlapping hashes and compare with hash of pattern
for (unsigned i = 0; i < length(genome) - length(myShape) + 1; ++i)
if (hash(myShape, begin(genome) + i) == hashedPattern)
std::cout << "Hit at position: " << i << std::endl;
return 0;
}
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