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#include <iostream>
#include <seqan/consensus.h>
#include <seqan/sequence.h>
#include <seqan/store.h>
using namespace seqan2;
int main()
{
// Reference to simulate reads from.
Dna5String ref =
"AATGGATGGCAAAATAGTTGTTCCATGAATACATCTCTAAAGAGCTTTGATGCTAATTTAGTCAAATTTT"
"CAATACTGTACAATCTTCTCTAGAGCAGAGCAAAAGAATAAAAGCACTTCTAGCTAATATTATGTGGCAT";
// Read length and step width for reads.
int const READ_LENGTH = 50;
int const STEP = 5;
// Compute reads and append to FragmentStore.
FragmentStore<> store;
for (unsigned pos = 0, i = 0; pos + READ_LENGTH < length(ref); pos += STEP, ++i)
{
// Append a new read sequence.
unsigned readID = appendRead(store, infix(ref, pos, pos + READ_LENGTH));
// Create small perturbation of the position but not left of position 0.
int pos2 = std::max(0, (int)pos + ((int)i % 6 - 3));
// Append a new read alignment for the just added read.
appendAlignedRead(store, readID, 0, pos2, pos2 + READ_LENGTH);
}
// Add contig and contig name for printing.
resize(store.contigStore, 1);
store.contigStore[0].seq = ref;
resize(store.contigNameStore, 1);
// Print initial perturbated alignment.
std::cout << "Initial Alignment\n\n";
AlignedReadLayout layout;
layoutAlignment(layout, store);
printAlignment(std::cout, layout, store, /*contigID=*/ 0,
/*beginPos=*/ 0, /*endPos=*/ (int)length(ref), 0, 30);
// Compute consensus alignment.
ConsensusAlignmentOptions options;
consensusAlignment(store, options);
// Print final consensus alignment.
std::cout << "\n\nFinal Consensus Alignment\n\n";
layoutAlignment(layout, store);
printAlignment(std::cout, layout, store, /*contigID=*/ 0,
/*beginPos=*/ 0, /*endPos=*/ (int)length(ref), 0, 30);
return 0;
}
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