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#include "spoa/spoa.hpp"
#define PYBIND11_DETAILED_ERROR_MESSAGES // for type information in casting errors
#include <pybind11/stl.h>
#include <pybind11/pybind11.h>
using namespace pybind11::literals; // for _a in pybind def
auto poa(std::vector<std::string> sequences, int algorithm, bool genmsa,
int m, int n, int g, int e, int q, int c, pybind11::object min_coverage) -> pybind11::tuple
{
// set min_coverage to the default of the SPOA CLI (-1) if None
int min_cov = -1;
if (min_coverage != pybind11::none()) {
min_cov = min_coverage.cast<int>();
}
auto alignment_engine = spoa::AlignmentEngine::Create(
static_cast<spoa::AlignmentType>(algorithm), m, n, g, e, q, c
);
spoa::Graph graph{};
for (const auto& it: sequences) {
auto alignment = alignment_engine->Align(it, graph);
graph.AddAlignment(alignment, it);
}
auto consensus = graph.GenerateConsensus(min_cov);
std::vector<std::string> msa;
if (genmsa)
msa = graph.GenerateMultipleSequenceAlignment();
return pybind11::make_tuple(consensus, msa);
}
PYBIND11_MODULE(spoa, m) {
m.def(
"poa", &poa, "",
"sequences"_a, "algorithm"_a=0, "genmsa"_a=true,
"m"_a=5, "n"_a=-4, "g"_a=-8, "e"_a=-6, "q"_a=-10, "c"_a=-4,
"min_coverage"_a=pybind11::none()
);
m.attr("__version__") = VERSION_INFO;
}
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