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# Copyright 2017 Google LLC.
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from "deepvariant/protos/deepvariant_pyclif.h" import *
from "deepvariant/python/allelecounter.h" import *
from "third_party/nucleus/io/python/vcf_reader.h" import *

from "deepvariant/variant_calling.h":
  namespace `learning::genomics::deepvariant::vcf_candidate_importer`:
    class VariantCaller:
      def __init__(self, options: VariantCallerOptions)
      def `CallsFromAlleleCounter` as calls_from_allele_counter(
          self, allele_counter: AlleleCounter) -> list<DeepVariantCall>
      def `CallsFromVcf` as calls_from_vcf(
          self, allele_counter: AlleleCounter, vcf_reader: VcfReader) -> list<DeepVariantCall>
      def `CallPositionsFromVcf` as call_positions_from_vcf(
          self, allele_counter: AlleleCounter, vcf_reader: VcfReader) -> list<int>