Exemplos de AlphaCount64::getMaxDNABase em C++ (Cpp)

Exemplo n.º 1

Arquivo: preqc.cpp Projeto: richarddurbin/sga

std::string get_valid_dbg_neighbors_coverage_and_ratio(const std::string& kmer,
                                                       const BWTIndexSet& index_set,
                                                       size_t min_coverage,
                                                       double min_ratio,
                                                       EdgeDir dir)
{
    std::string out;
    AlphaCount64 counts = 
        BWTAlgorithms::calculateDeBruijnExtensionsSingleIndex(kmer, 
                                                              index_set.pBWT,
                                                              dir,
                                                              index_set.pCache);
    
    if(!counts.hasDNAChar())
        return out; // no extensions

    char max_b = counts.getMaxDNABase();
    size_t max_c = counts.get(max_b);

    for(size_t j = 0; j < 4; ++j)
    {
        char b = "ACGT"[j];
        size_t c = counts.get(b);
        if(c >= min_coverage && (double)c / max_c >= min_ratio)
            out.push_back(b);
    }
    return out;    
}