mono/multi-molecular integrator usage

example.cpp

// monomolecular
string mdl = "P6C4.NoCov"; // maybe we should just have a default model for each chemistry? e.g. just "P6C4"?
IntegratorConfig icfg; // ParameterTable::Default, minZScore=-5
string tpl = ...; // do POA
vector<string> reads = ...;
vector<tuple<size_t, size_t>> extents = ...; // get extents from POA
SNR snr = { ..., ..., ..., ... };
MonoMolecularIntegrator mmi(tpl, icfg, snr, mdl);
for (size_t i = 0; i < reads.size(); ++i)
{
    size_t ts, te;
    tie(ts, te) = extents[i];
    auto error = mmi.AddRead(MappedRead(Read(std::to_string(i), reads[i], mdl), ts, te));
    // do something with error maybe?
}
PolishConfig pcfg;
Polish(mmi, pcfg);
return ConsensusAndQVs(mmi);

// multimolecular
IntegratorConfig icfg;
vector<tuple<string, SNR, string>> reads = ...; // seq, SNR, model
string tpl = ...; // Poa
vector<tuple<size_t, size_t>> extents = ...; // also from Poa? or by lifting coordinates like Quiver
MultiMolecularIntegrator mmi(tpl, icfg);
for (size_t i = 0; i < reads.size(); ++i)
{
    size_t ts, te;
    tie(ts, te) = extents[i];
    auto status = mmi.AddRead(MappedRead(Read(std::to_string(i), get<0>(reads[i]), get<2>(reads[i])), ts, te), get<1>(reads[i]));
}
PolishConfig pcfg;
Polish(mmi, pcfg);
return ConsensusAndQVs(mmi);

One more thought: presumably, in the future, we could save memory by making the "multi" be an aggregate over "mono" --- combine subreads by ZMW into mono's.

We could use a bucket of templates keyed on SNR to do things transparently at the Integrator level, and be done with this distinction, true.