C++ (Cpp) GuidedAlign Examples

Example #1

File: SimpleAligner.cpp Project: ffrancis/pbdagcon

void SimpleAligner::align(dagcon::Alignment& aln) {
    // This alignment type defined in blasr code base
    blasr::Alignment initialAln, refinedAln;
    FASTQSequence query;
    query.seq = (Nucleotide*)aln.qstr.c_str();
    query.length = aln.qstr.length();

    DNASequence target;
    target.seq = (Nucleotide*)aln.tstr.c_str();
    target.length = aln.tstr.length();
    SDPAlign(query, target, distScoreFn_, tupleMetrics_.tupleSize,
             config_.sdpIndel, config_.sdpIndel, config_.indelRate*2,
             initialAln, Local);

    GuidedAlign(query, target, initialAln, distScoreFn_, 
        config_.bandSize, refinedAln);

    std::string queryStr, alignStr, targetStr;

    //StickPrintAlignment(initialAln, query, target, std::cout);
    //StickPrintAlignment(refinedAln, query, target, std::cout);

    CreateAlignmentStrings(refinedAln, query.seq, target.seq, 
            targetStr, alignStr, queryStr, query.length, target.length);

    // alignment coordinates may change, update alignment object
    aln.start += refinedAln.GenomicTBegin();
    aln.end = aln.start + refinedAln.GenomicTEnd();

    if (aln.strand == '-') {
        aln.start = aln.tlen - aln.end;
        aln.qstr = revComp(queryStr);
        aln.tstr = revComp(targetStr);
    } else {
        aln.qstr = queryStr;
        aln.tstr = targetStr;
    }
    aln.start++;
}

Example #2

File: SimpleAligner.cpp Project: Magdoll/ICE

void SimpleAligner::align(dagcon::Alignment& aln) {
    // This alignment type defined in blasr code base
    blasr::Alignment initialAln, refinedAln;
    FASTQSequence query;
    query.seq = (Nucleotide*)aln.qstr.c_str();
    query.length = aln.qstr.length();
    query.AllocateRichQualityValues(query.length);
    query.qual.Allocate(query.length);

    DNASequence target;
    target.seq = (Nucleotide*)aln.tstr.c_str();
    target.length = aln.tstr.length();
    SDPAlign(query, target, distScoreFn_, tupleMetrics_.tupleSize,
             config_.sdpIndel, config_.sdpIndel, config_.indelRate*2,
             initialAln, Local);

    GuidedAlign(query, target, initialAln, distScoreFn_, 
        config_.bandSize, refinedAln);

    //StickPrintAlignment(initialAln, query, target, std::cout);
    //StickPrintAlignment(refinedAln, query, target, std::cout);

    std::string queryStr, alignStr, targetStr;
    CreateAlignmentStrings(refinedAln, query.seq, target.seq, 
            targetStr, alignStr, queryStr, query.length, target.length);

    if (aln.strand == '-') {
        aln.start = aln.len - (aln.end + refinedAln.tPos);
        aln.qstr = revComp(queryStr);
        aln.tstr = revComp(targetStr);
    } else {
        aln.start += refinedAln.tPos;
        aln.qstr = queryStr;
        aln.tstr = targetStr;
    }
    aln.start++;
}