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#include <alignment/format/SummaryPrinter.hpp>
void SummaryOutput::Print(AlignmentCandidate<DNASequence, FASTQSequence> &alignment,
std::ostream &outFile)
{
int lastBlock = alignment.blocks.size() - 1;
outFile << alignment.qName << " " << alignment.tName << " " << alignment.qStrand << " "
<< alignment.tStrand << " " << alignment.score << " " << alignment.pctSimilarity << " "
<< alignment.tAlignedSeqPos + alignment.blocks[0].tPos << " "
<< alignment.tAlignedSeqPos + alignment.blocks[lastBlock].tPos +
alignment.blocks[lastBlock].length
<< " " << alignment.tLength << " "
<< alignment.qAlignedSeqPos + alignment.blocks[0].qPos << " "
<< alignment.qAlignedSeqPos + alignment.blocks[lastBlock].qPos +
alignment.blocks[lastBlock].length
<< " " << alignment.qLength << " " << alignment.nCells << std::endl;
}
void SummaryOutput::PrintHeader(std::ostream &out)
{
out << "qName tName qStrand tStrand score percentSimilarity tStart tEnd tLength qStart qEnd "
"qLength nCells"
<< std::endl;
}
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