# 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.Variant do
  @moduledoc """
  A variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set.  Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related calls typically from one sample.

  ## Attributes

  - info (%{optional(String.t) => [ErrorUnknown]}): A map of additional variant information. This must be of the form map<string, string[]> (string key mapping to a list of string values). Defaults to: `null`.
  - alternateBases ([String.t]): The bases that appear instead of the reference bases. Defaults to: `null`.
  - calls ([VariantCall]): The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant. Defaults to: `null`.
  - created (String.t): The date this variant was created, in milliseconds from the epoch. Defaults to: `null`.
  - end (String.t): The end position (0-based) of this variant. This corresponds to the first base after the last base in the reference allele. So, the length of the reference allele is (end - start). This is useful for variants that don't explicitly give alternate bases, for example large deletions. Defaults to: `null`.
  - filter ([String.t]): A list of filters (normally quality filters) this variant has failed. `PASS` indicates this variant has passed all filters. Defaults to: `null`.
  - id (String.t): The server-generated variant ID, unique across all variants. Defaults to: `null`.
  - names ([String.t]): Names for the variant, for example a RefSNP ID. Defaults to: `null`.
  - quality (float()): A measure of how likely this variant is to be real. A higher value is better. Defaults to: `null`.
  - referenceBases (String.t): The reference bases for this variant. They start at the given position. Defaults to: `null`.
  - referenceName (String.t): The reference on which this variant occurs. (such as `chr20` or `X`) Defaults to: `null`.
  - start (String.t): The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases. Defaults to: `null`.
  - variantSetId (String.t): The ID of the variant set this variant belongs to. Defaults to: `null`.
  """

  use GoogleApi.Gax.ModelBase

  @type t :: %__MODULE__{
          :info => map(),
          :alternateBases => list(any()),
          :calls => list(GoogleApi.Genomics.V1.Model.VariantCall.t()),
          :created => any(),
          :end => any(),
          :filter => list(any()),
          :id => any(),
          :names => list(any()),
          :quality => any(),
          :referenceBases => any(),
          :referenceName => any(),
          :start => any(),
          :variantSetId => any()
        }

  field(:info, type: :map)
  field(:alternateBases, type: :list)
  field(:calls, as: GoogleApi.Genomics.V1.Model.VariantCall, type: :list)
  field(:created)
  field(:end)
  field(:filter, type: :list)
  field(:id)
  field(:names, type: :list)
  field(:quality)
  field(:referenceBases)
  field(:referenceName)
  field(:start)
  field(:variantSetId)
end

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

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