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// The comment lines containing ![fragment-line] are there for the
// documentation system. You can ignore them when reading this file.
//![full]
//![top]
#include <iostream>
#include <seqan/sequence.h>
#include <seqan/stream.h>
using namespace seqan2;
// Function to print simple alignment between two sequences with the same length
// .. for two sequences of different types
template <typename TText1, typename TText2>
void printAlign(TText1 const & genomeFragment, TText2 const & read)
{
std::cout << "Alignment " << std::endl;
std::cout << " genome : ";
std::cout << genomeFragment << std::endl;
std::cout << " read : ";
std::cout << read << std::endl;
}
int main()
{
// We have given a genome sequence
Dna5String genome = "ATGGTTTCAACGTAATGCTGAACATGTCGCGT";
// A read sequence
Dna5String read = "TGGTNTCA";
// And the begin position of a given alignment between the read and the genome
unsigned beginPosition = 1;
//![top]
// Create Infix of type Dna5String and get the corresponding infix sequence of genome
Infix<Dna5String>::Type genomeFragment = infix(genome, beginPosition, beginPosition + length(read));
//![bottom]
// Call of our function to print the simple alignment
printAlign(genomeFragment, read);
return 0;
}
//![bottom]
//![full]
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