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//![includes]
#include <iostream>
#include <seqan/store.h>
#include <seqan/consensus.h>
using namespace seqan2;
int main()
{
//![includes]
//![fill_store]
FragmentStore<> store;
// Resize contigStore and contigNameStore (required for printing the first layout).
resize(store.contigStore, 1);
appendValue(store.contigNameStore, "ref");
// 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");
// The position used in the following are only approximate and would
// not lead to the read layout above.
appendAlignedRead(store, 0, 0, 0, (int)length(store.readSeqStore[0]));
appendAlignedRead(store, 1, 0, 12, 12 + (int)length(store.readSeqStore[1]));
appendAlignedRead(store, 2, 0, 14, 14 + (int)length(store.readSeqStore[2]));
appendAlignedRead(store, 3, 0, 18, 18 + (int)length(store.readSeqStore[3]));
appendAlignedRead(store, 4, 0, 25, 25 + (int)length(store.readSeqStore[4]));
// Print the (wrong) alignment.
std::cout << "Initial alignment\n\n";
AlignedReadLayout layout;
layoutAlignment(layout, store);
printAlignment(std::cout, layout, store, /*contigID=*/ 0, /*beginPos=*/ 0, /*endPos=*/ 80, 0, 30);
//![fill_store]
//![compute_consensus]
ConsensusAlignmentOptions options;
options.useContigID = true;
consensusAlignment(store, options);
//![compute_consensus]
//![print_layout]
std::cout << "Final alignment\n\n";
layoutAlignment(layout, store);
printAlignment(std::cout, layout, store, /*contigID=*/ 0, /*beginPos=*/ 0, /*endPos=*/ 80, 0, 30);
return 0;
}
//![print_layout]
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