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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 "third_party/nucleus/util/proto_clif_converter.h" import *

from "deepvariant/variant_calling_multisample.h":
  namespace `learning::genomics::deepvariant::multi_sample`:
    class VariantCaller:
      def __init__(self, options: VariantCallerOptions)
      def `CallsFromAlleleCounts` as calls_from_allele_counts(
          self, allele_counters: dict<str, AlleleCounter>, target_sample: str) -> list<DeepVariantCall>
      def `CallPositionsFromAlleleCounts` as call_positions_from_allele_counts(
          self, allele_counters: dict<str, AlleleCounter>, target_sample: str) -> list<int>