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- // 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);
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