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);
}
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;
}