Exemplos de known_pos_range2::size em C++ (Cpp)

Exemplo n.º 1

Arquivo: SVScorer.cpp Projeto: avilella/manta

unsigned
SVScorer::
getBreakendMaxMappedDepth(const SVBreakend& bp)
{
    /// define a new interval -/+ 50 bases around the center pos
    /// of the breakpoint
    static const pos_t regionSize(50);
    const pos_t centerPos(bp.interval.range.center_pos());
    const known_pos_range2 searchRange(std::max((centerPos-regionSize),0), (centerPos+regionSize));

    std::vector<unsigned> depth(searchRange.size(),0);

    bool isNormalFound(false);

    const unsigned bamCount(_bamStreams.size());
    for (unsigned bamIndex(0); bamIndex < bamCount; ++bamIndex)
    {
        if (_isAlignmentTumor[bamIndex]) continue;

        bam_streamer& bamStream(*_bamStreams[bamIndex]);

        // set bam stream to new search interval:
        bamStream.set_new_region(bp.interval.tid, searchRange.begin_pos(), searchRange.end_pos());

        while (bamStream.next())
        {
            const bam_record& bamRead(*(bamStream.get_record_ptr()));

            // turn filtration off down to mapped only to match depth estimate method:
            //if (_readScanner.isReadFiltered(bamRead)) continue;
            if (bamRead.is_unmapped()) continue;

            if ((bamRead.pos()-1) >= searchRange.end_pos()) break;

            addReadToDepthEst(bamRead,searchRange.begin_pos(),depth);
        }

        isNormalFound=true;
        break;
    }

    assert(isNormalFound);

    return *(std::max_element(depth.begin(),depth.end()));
}

Exemplo n.º 2

Arquivo: SVScorer.cpp Projeto: aminzia/manta

void
SVScorer::
getBreakendMaxMappedDepthAndMQ0(
    const bool isMaxDepth,
    const double cutoffDepth,
    const SVBreakend& bp,
    unsigned& maxDepth,
    float& MQ0Frac)
{
    /// define a new interval -/+ 50 bases around the center pos
    /// of the breakpoint
    static const pos_t regionSize(50);

    maxDepth=0;
    MQ0Frac=0;

    unsigned totalReads(0);
    unsigned totalMQ0Reads(0);

    const pos_t centerPos(bp.interval.range.center_pos());
    const known_pos_range2 searchRange(std::max((centerPos-regionSize),0), (centerPos+regionSize));

    if (searchRange.size() == 0) return;

    std::vector<unsigned> depth(searchRange.size(),0);

    bool isCutoff(false);
    bool isNormalFound(false);

    const unsigned bamCount(_bamStreams.size());
    for (unsigned bamIndex(0); bamIndex < bamCount; ++bamIndex)
    {
        if (_isAlignmentTumor[bamIndex]) continue;
        isNormalFound=true;

        bam_streamer& bamStream(*_bamStreams[bamIndex]);

        // set bam stream to new search interval:
        bamStream.set_new_region(bp.interval.tid, searchRange.begin_pos(), searchRange.end_pos());

        while (bamStream.next())
        {
            const bam_record& bamRead(*(bamStream.get_record_ptr()));

            // turn filtration down to mapped only to match depth estimate method:
            if (bamRead.is_unmapped()) continue;

            const pos_t refPos(bamRead.pos()-1);
            if (refPos >= searchRange.end_pos()) break;

            addReadToDepthEst(bamRead,searchRange.begin_pos(),depth);

            totalReads++;
            if (0 == bamRead.map_qual()) totalMQ0Reads++;

            if (isMaxDepth)
            {
                const pos_t depthOffset(refPos-searchRange.begin_pos());
                if (depthOffset>=0)
                {
                    if (depth[depthOffset] > cutoffDepth)
                    {
                        isCutoff=true;
                        break;
                    }
                }
            }
        }

        if (isCutoff) break;
    }

    assert(isNormalFound);

    maxDepth = *(std::max_element(depth.begin(),depth.end()));
    if (totalReads>=10)
    {
        MQ0Frac = static_cast<float>(totalMQ0Reads)/static_cast<float>(totalReads);
    }
}