Esempio n. 1
0
reference::ReferencePosition getAlignmentPositionFromName(const std::size_t readNumber, const FragmentMetadata &fragment)
{
    // numbers are 1-based
    const auto name = getReadName(readNumber - 1, fragment);

    if (name.second == name.first)
    {
        return reference::ReferencePosition(reference::ReferencePosition::TooManyMatch);
    }

    if ('u' == *name.first)
    {
        ISAAC_ASSERT_MSG(false, common::makeFastIoString(fragment.getCluster().nameBegin(), fragment.getCluster().nameEnd()) << " " << fragment);
        return reference::ReferencePosition(reference::ReferencePosition::NoMatch);
    }
    return reference::ReferencePosition(
        std::atol(&*name.first + 2),
        std::atol(&*std::find(name.first + 2, name.second, ':') + 1),
        false,
        'r' == *name.first);
}
Esempio n. 2
0
std::pair<BclClusters::const_iterator, BclClusters::const_iterator> getReadName(const std::size_t readIndex, const FragmentMetadata &fragment)
{
    std::pair<BclClusters::const_iterator, BclClusters::const_iterator> ret = {fragment.getCluster().nameBegin(), fragment.getCluster().nameEnd()};
    if (ret.second == ret.first)
    {
        return ret;
    }

    if (!readIndex)
    {
        ret.first = fragment.getCluster().nameBegin();
        ret.second = std::find(fragment.getCluster().nameBegin(), fragment.getCluster().nameEnd(), '-');
    }
    else
    {
        ret.first = std::find(fragment.getCluster().nameBegin(), fragment.getCluster().nameEnd(), '-') + 1;
        ret.second = fragment.getCluster().nameEnd();
    }

    return ret;
}