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#include <alignment/format/IntervalPrinter.hpp>
void IntervalOutput::Print(T_AlignmentCandidate &alignment, std::ostream &outFile)
{
int mapQV = alignment.mapQV;
int lastBlock = alignment.blocks.size() - 1;
if (lastBlock < 0) return;
outFile << alignment.qName << " " << alignment.tName << " " << alignment.score << " "
<< alignment.pctSimilarity << " " << alignment.qStrand << " " << alignment.QAlignStart()
<< " " << alignment.QAlignEnd() << " " << alignment.qLength << " " << alignment.tStrand
<< " " << alignment.TAlignStart() << " "
<< (alignment.tAlignedSeqPos + alignment.tPos + alignment.blocks[lastBlock].tPos +
alignment.blocks[lastBlock].length)
<< " " << alignment.tLength << " " << mapQV << std::endl;
//Remove the last four fields from m4 format.
//<< " " << alignment.nCells << " " << alignment.clusterScore
//<< " " << alignment.probScore << " "
//<< alignment.numSignificantClusters
}
// Print an alignment from a sam file in Interval (m 4) format.
void IntervalOutput::PrintFromSAM(AlignmentCandidate<> &alignment, std::ostream &outFile)
{
int mapQV = alignment.mapQV;
int lastBlock = alignment.blocks.size() - 1;
if (lastBlock < 0) return;
outFile << alignment.qName << " " << alignment.tName << " " << alignment.score << " "
<< alignment.pctSimilarity << " " << alignment.qStrand << " " << alignment.QAlignStart()
<< " " << alignment.QAlignEnd() << " " << alignment.qLength << " " << alignment.tStrand
<< " ";
DNALength tS = alignment.TAlignStart();
DNALength tE = alignment.tAlignedSeqPos + alignment.tPos + alignment.blocks[lastBlock].tPos +
alignment.blocks[lastBlock].length;
if (alignment.tStrand == 1) {
// Since the alignment is from a SAM file and the reference
// is reverse, compute tS and tE in the coordinate of the reverse
// complementary sequence
DNALength tmp = tS;
tS = alignment.tLength - tE;
tE = alignment.tLength - tmp;
}
outFile << tS << " " << tE << " " << alignment.tLength << " " << mapQV << std::endl;
}
void IntervalOutput::PrintHeader(std::ostream &out)
{
out << "qName tName score percentSimilarity qStrand "
<< "qStart qEnd qLength tStrand tStart tEnd tLength mapQV" << std::endl;
//ncells clusterScore probscore numSigClusters" << std::endl;
}
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