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from "deepvariant/protos/deepvariant_pyclif.h" import *
from "third_party/nucleus/util/proto_clif_converter.h" import *
from "third_party/nucleus/protos/reads_pyclif.h" import *

from "deepvariant/direct_phasing.h":
  namespace `learning::genomics::deepvariant`:
    class PhasedVariant:
      position: int
      phase_1_bases: str
      phase_2_bases: str

    class DirectPhasing:
      def __init__(self)
      def `GraphViz` as graphviz(self) -> str
      def `GetPhasedVariants` as get_phased_variants(self) -> list<PhasedVariant>
      def `PhaseReadsPython` as phase(self, candidates: list<DeepVariantCall>,
                           reads: list<ConstProtoPtr<Read>>) -> list<int>