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#include <iostream>
#include <seqan/store.h>
#include <seqan/consensus.h>
using namespace seqan;
int main()
{
FragmentStore<> store;
// Actual read layout.
//
// AATGGATGGCAAAATAGTTGTTCCATGAATACATCTCTAAAGAGCTTT
// AAAATAGTTGTTCCATGAATACATCTCTAAAGAGCTTTGATGCTAATTT
// AGTTGTTCCATGAATACATCTCTAAAGAGCTTTGATGCTAATTTAGTCAAATTTTCAATACTGTA
// ACATCTCTAAAGAGCTTTGATGCTAATTTAGTCAAATT
// AGAGCTTTGATGCTAATTTAGTCAAATTTTCAATACTGTACAATCTTCTCTAG
// Append reads (includes small errors).
appendRead(store, "AATGGATGGCAAAATAGTTGTTCCATGAATACATCTCTAAAGAGCTTT");
appendRead(store, "AAAGTAGTTGTTCCATGAATACATCTCTAAAGAGCTTTGATGCTAATTT");
appendRead(store, "AGTTGTCCATGAATACATCTCTAAAGAGCTTTGATGCTAATTTAGTCAATTTTCAATACTGTA");
appendRead(store, "ACATCTCTTAAAGAGCTTTGATGCTAATTTAGTCAAATT");
appendRead(store, "AGAGCTTTGATGCTAATTTAGTCAAATTTTCAATACTGTACAATCTTCTCTAG");
ConsensusAlignmentOptions options;
options.useContigID = false;
consensusAlignment(store, options);
std::cout << "Final alignment\n\n";
AlignedReadLayout layout;
layoutAlignment(layout, store);
printAlignment(std::cout, layout, store, /*contigID=*/ 0, /*beginPos=*/ 0, /*endPos=*/ 80, 0, 30);
return 0;
}
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