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

from "deepvariant/pileup_image_native.h":
  namespace `learning::genomics::deepvariant`:
    class PileupImageEncoderNative:

      def __init__(self, options: PileupImageOptions)

      def `AllChannelsEnum` as all_channels_enum(
          self, alt_aligned_pileup: str) -> list<DeepVariantChannelEnum>

      def `EncodeReadPython` as encode_read(
          self,
          dv_call: ConstProtoPtr<DeepVariantCall>,
          ref_bases: str,
          read: ConstProtoPtr<Read>,
          image_start_pos: int,
          alt_alleles: list<str>) -> ImageRow

      def `EncodeReference` as encode_reference(
          self, ref_bases: str) -> ImageRow

      def `BaseColor` as base_color(self, base: str) -> int

      def `StrandColor` as strand_color(
          self, on_positive_strand: bool) -> int

      def `SupportsAltColor` as supports_alt_color(
          self, read_supports_alt: int) -> int

      def `MatchesRefColor` as matches_ref_color(
          self, base_matches_ref: bool) -> int

      def `BaseQualityColor` as base_quality_color(
          self, base_qual: int) -> int

      def `MappingQualityColor` as mapping_quality_color(
          self, mapping_qual: int) -> int

      def `AlleleFrequencyColor` as allele_frequency_color(
          self, allele_frequency: float) -> int