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#include <iostream>
#include <seqan/store.h>
using namespace seqan;
int main()
{
// instantiate emtpy FragmentStore and set file paths
FragmentStore<> store;
std::string pathGenome = getAbsolutePath("/demos/tutorial/store/ex1.fa");
std::string pathSAM = getAbsolutePath("/demos/tutorial/store/ex1.sam");
// load example genome and example reads and alignments
loadContigs(store, pathGenome.c_str());
BamFileIn bamFile(pathSAM.c_str());
readRecords(store, bamFile);
// compute staircase read layout and print from position 30..129
AlignedReadLayout layout;
layoutAlignment(layout, store);
printAlignment(std::cout, layout, store, 1, 30, 130, 0, 36);
return 0;
}
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