struct

  type t = {
    name: string;
    parameters: (string * string) list
  }
  let name t = t.name
  let to_json {name; parameters}: Yojson.Basic.json =
    `Assoc [
      "name", `String name;
      "parameters",
      `Assoc (List.map parameters ~f:(fun (a, b) -> a, `String b));
    ]

  let generate_config_file ~path config : KEDSL.Program.t =
    let open KEDSL in
    Program.(
      shf "echo '[user]' > %s" path
      && chain
        (List.map config.parameters (fun (k, v) ->
             shf "echo '%s = %s' >> %s" k v path))
    )

  let default =
    { name = "default";
      parameters = [
        "isSkipDepthFilters", "0";
        "maxInputDepth", "10000";
        "depthFilterMultiple", "3.0";
        "snvMaxFilteredBasecallFrac", "0.4";
        "snvMaxSpanningDeletionFrac", "0.75";
        "indelMaxRefRepeat", "8";
        "indelMaxWindowFilteredBasecallFrac", "0.3";
        "indelMaxIntHpolLength", "14";
        "ssnvPrior", "0.000001";
        "sindelPrior", "0.000001";
        "ssnvNoise", "0.0000005";
        "sindelNoise", "0.0000001";
        "ssnvNoiseStrandBiasFrac", "0.5";
        "minTier1Mapq", "40";
        "minTier2Mapq", "5";
        "ssnvQuality_LowerBound", "15";
        "sindelQuality_LowerBound", "30";
        "isWriteRealignedBam", "0";
        "binSize", "25000000";
        "extraStrelkaArguments", "--eland-compatibility";
      ]}
  let test1 =
    { name = "test1";
      parameters = [
        "isSkipDepthFilters", "0";
        "maxInputDepth", "10000";
        "depthFilterMultiple", "3.0";
        "snvMaxFilteredBasecallFrac", "0.4";
        "snvMaxSpanningDeletionFrac", "0.75";
        "indelMaxRefRepeat", "8";
        "indelMaxWindowFilteredBasecallFrac", "0.3";
        "indelMaxIntHpolLength", "14";
        "ssnvPrior", "0.000001";
        "sindelPrior", "0.000001";
        "ssnvNoise", "0.0000005";
        "sindelNoise", "0.0000001";
        "ssnvNoiseStrandBiasFrac", "0.5";
        "minTier1Mapq", "40";
        "minTier2Mapq", "5";
        "ssnvQuality_LowerBound", "15";
        "sindelQuality_LowerBound", "30";
        "isWriteRealignedBam", "0";
        "binSize", "25000000";
        "extraStrelkaArguments", "--eland-compatibility";
        "priorSomaticSnvRate", "1e-06";
        "germlineSnvTheta", "0.001";
      ]}
  let empty_exome =
    { name = "empty-exome";
      parameters = [
        "isSkipDepthFilters", "1";
      ]}
  let exome_default =
    { name = "exome-default";
      parameters = [
        "isSkipDepthFilters", "1";
        "maxInputDepth", "10000";
        "depthFilterMultiple", "3.0";
        "snvMaxFilteredBasecallFrac", "0.4";
        "snvMaxSpanningDeletionFrac", "0.75";
        "indelMaxRefRepeat", "8";
        "indelMaxWindowFilteredBasecallFrac", "0.3";
        "indelMaxIntHpolLength", "14";
        "ssnvPrior", "0.000001";
        "sindelPrior", "0.000001";
        "ssnvNoise", "0.0000005";
        "sindelNoise", "0.0000001";
        "ssnvNoiseStrandBiasFrac", "0.5";
        "minTier1Mapq", "40";
        "minTier2Mapq", "5";
        "ssnvQuality_LowerBound", "15";
        "sindelQuality_LowerBound", "30";
        "isWriteRealignedBam", "0";
        "binSize", "25000000";
        "extraStrelkaArguments", "--eland-compatibility";
      ]}

end