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# Copyright 2017 Google LLC.
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from "deepvariant/protos/deepvariant_pyclif.h" import *
from "third_party/nucleus/io/python/reference.h" import *
from "third_party/nucleus/protos/range_pyclif.h" import *
from "third_party/nucleus/protos/reads_pyclif.h" import *
from "third_party/nucleus/util/proto_clif_converter.h" import *
from "third_party/nucleus/protos/cigar_pyclif.h" import *

from "deepvariant/allelecounter.h":
  namespace `learning::genomics::deepvariant`:
    class AlleleCounter:
      def __init__(self,
                   ref: GenomeReference,
                   interval: Range,
                   candidate_positions: list<int>,
                   options: AlleleCounterOptions)
      @add__init__
      def Default(self,
                   ref: GenomeReference,
                   interval: Range,
                   reads_interval: Range,
                   candidate_positions: list<int>,
                   options: AlleleCounterOptions)
      def `AddPython` as add(self, read: ConstProtoPtr<Read>, sample: str)
      def `NormalizeAndAddPython` as normalize_and_add(self, read: ConstProtoPtr<Read>, sample: str) -> (cigar: list<CigarUnit>, shift: int)
      def `Counts` as counts(self) -> list<AlleleCount>
      def `SummaryCounts` as summary_counts(self, left_padding: int = default, right_padding: int = default) -> list<AlleleCountSummary>