/** enqueue a set of variants */
void VariantCallsOnly::add(Variants const & v)
{
if (_impl->buffered_variants.size() > 0 &&
v.chr == _impl->buffered_variants.back().chr &&
v.pos < _impl->buffered_variants.back().pos)
{
error("Variant added out of order at %s:%i / %i", v.chr.c_str(), v.pos, _impl->buffered_variants.back().pos);
}
#ifdef DEBUG_VARIANTCALLSONLY
std::cerr << "Variants added: " << v << "\n";
#endif
if (v.anyHomref())
{
Variants non_hr = v;
int n_non_hr = v.calls.size();
for (size_t q = 0; q < v.calls.size(); ++q)
{
if(v.calls[q].isHomref())
{
non_hr.calls[q] = Call();
_impl->homref_ivs.addInterval(v.pos, v.pos + v.len - 1, q);
// remember dp
if(q >= _impl->homref_dp.size())
{
_impl->homref_dp.resize(q+1);
}
_impl->homref_dp[q].set(v.calls[q].dp, v.pos, v.pos + v.len - 1);
// remember gq
if(q >= _impl->homref_gq.size())
{
_impl->homref_gq.resize(q+1);
}
_impl->homref_gq[q].set(v.calls[q].gq, v.pos, v.pos + v.len - 1);
--n_non_hr;
}
else if(v.calls[q].isNocall())
{
--n_non_hr;
}
}
if (n_non_hr || non_hr.anyAmbiguous())
{
#ifdef DEBUG_VARIANTCALLSONLY
std::cerr << "non-hr-add: " << v << "\n";
#endif
_impl->buffered_variants.push_back(non_hr);
}
}
else
{
#ifdef DEBUG_VARIANTCALLSONLY
std::cerr << "non-hr-pass-on: " << v << "\n";
#endif
_impl->buffered_variants.push_back(v);
}
}
bool test(Variants const & v) { return v.anyHomref(); }
