void ReadAlignment(int alignmentIndex, AlignmentCandidate<FASTASequence, FASTASequence> &alignment) {
CmpAlignment cmpAln;
ReadAlignment(alignmentIndex, cmpAln);
string refSequence;
string readSequence;
readSequence.resize(cmpAln.alignmentArray.size());
refSequence.resize(cmpAln.alignmentArray.size());
ByteAlignmentToQueryString(&cmpAln.alignmentArray[0], cmpAln.alignmentArray.size(), &readSequence[0]);
ByteAlignmentToRefString(&cmpAln.alignmentArray[0], cmpAln.alignmentArray.size(), &refSequence[0]);
string ungappedRead, ungappedRef;
RemoveGaps(readSequence, ungappedRead);
RemoveGaps(refSequence, ungappedRef);
GappedStringsToAlignment(readSequence, refSequence, alignment);
FASTASequence qAlignedSeq, rAlignedSeq;
qAlignedSeq.seq = (Nucleotide*) &ungappedRead[0];
qAlignedSeq.length = ungappedRead.size();
rAlignedSeq.seq = (Nucleotide*) &ungappedRef[0];
rAlignedSeq.length = ungappedRef.size();
alignment.tAlignedSeq.Copy(rAlignedSeq);
alignment.qAlignedSeq.Copy(qAlignedSeq);
unsigned int qStart = cmpAln.GetQueryStart();
unsigned int tStart = cmpAln.GetRefStart();
alignment.tPos = cmpAln.GetRefStart();
alignment.qPos = cmpAln.GetQueryStart();
alignment.nIns = cmpAln.GetNInsertions();
alignment.nDel = cmpAln.GetNDeletions();
alignment.nMatch = cmpAln.GetNMatch();
alignment.nMismatch=cmpAln.GetNMismatch();
alignment.qStrand= 0;
alignment.tStrand = cmpAln.GetTStrand();
alignment.pctSimilarity = ((float)alignment.nMatch) / (alignment.nMatch + alignment.nMismatch + alignment.nIns + alignment.nDel);
alignment.mapQV = cmpAln.GetMapQV();
}
