google_api_genomics

# Copyright 2017 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

# NOTE: This class is auto generated by the swagger code generator program.
# https://github.com/swagger-api/swagger-codegen.git
# Do not edit the class manually.

defmodule GoogleApi.Genomics.V1.Model.VariantCall do
  @moduledoc """
  A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345.

  ## Attributes

  - info (%{optional(String.t) => [ErrorUnknown]}): A map of additional variant call information. This must be of the form map<string, string[]> (string key mapping to a list of string values). Defaults to: `null`.
  - callSetId (String.t): The ID of the call set this variant call belongs to. Defaults to: `null`.
  - callSetName (String.t): The name of the call set this variant call belongs to. Defaults to: `null`.
  - genotype ([integer()]): The genotype of this variant call. Each value represents either the value of the `referenceBases` field or a 1-based index into `alternateBases`. If a variant had a `referenceBases` value of `T` and an `alternateBases` value of `[\"A\", \"C\"]`, and the `genotype` was `[2, 1]`, that would mean the call represented the heterozygous value `CA` for this variant. If the `genotype` was instead `[0, 1]`, the represented value would be `TA`. Ordering of the genotype values is important if the `phaseset` is present. If a genotype is not called (that is, a `.` is present in the GT string) -1 is returned. Defaults to: `null`.
  - genotypeLikelihood ([float()]): The genotype likelihoods for this variant call. Each array entry represents how likely a specific genotype is for this call. The value ordering is defined by the GL tag in the VCF spec. If Phred-scaled genotype likelihood scores (PL) are available and log10(P) genotype likelihood scores (GL) are not, PL scores are converted to GL scores.  If both are available, PL scores are stored in `info`. Defaults to: `null`.
  - phaseset (String.t): If this field is present, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls in the same reference sequence which have the same phaseset value. When importing data from VCF, if the genotype data was phased but no phase set was specified this field will be set to `*`. Defaults to: `null`.
  """

  use GoogleApi.Gax.ModelBase

  @type t :: %__MODULE__{
          :info => map(),
          :callSetId => any(),
          :callSetName => any(),
          :genotype => list(any()),
          :genotypeLikelihood => list(any()),
          :phaseset => any()
        }

  field(:info, type: :map)
  field(:callSetId)
  field(:callSetName)
  field(:genotype, type: :list)
  field(:genotypeLikelihood, type: :list)
  field(:phaseset)
end

defimpl Poison.Decoder, for: GoogleApi.Genomics.V1.Model.VariantCall do
  def decode(value, options) do
    GoogleApi.Genomics.V1.Model.VariantCall.decode(value, options)
  end
end

defimpl Poison.Encoder, for: GoogleApi.Genomics.V1.Model.VariantCall do
  def encode(value, options) do
    GoogleApi.Gax.ModelBase.encode(value, options)
  end
end