struct

  module Align = struct
    type t = {
      name: string;

      

(** The mapping quality MAPQ (column 5) is 255 for uniquely mapping reads, and int(-10*log10(1- 1/Nmap)) for multi-mapping reads. This scheme is same as the one used by TopHat and is compatible with Cufflinks. The default MAPQ=255 for the unique mappers maybe changed with to an integer between 0 and 255 to ensure compatibility with downstream tools such as GATK. *)


      sam_mapq_unique: int option;

      

(** Specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database. Ideally, this length should be equal to the ReadLength-1, where ReadLength is the length of the reads. *)


      overhang_length: int option;
      parameters: (string * string) list;
    }
    let name t = t.name

    let default = {
      name = "default";
      sam_mapq_unique = None;
      overhang_length = None;
      parameters = [];
    }

    let to_json t: Yojson.Basic.json =
      let {name;
           sam_mapq_unique;
           overhang_length;
           parameters} = t in
      `Assoc [
        "name", `String name;
        "sam_mapq_unique",
        (match sam_mapq_unique with
        | None -> `Null
        | Some x -> `Int x);
        "overhang_length",
        (match overhang_length with
        | None -> `Null
        | Some x -> `Int x);
        "parameters",
        `Assoc (List.map parameters ~f:(fun (a, b) -> a, `String b));
      ]

    let render {name;
                sam_mapq_unique;
                overhang_length;
                parameters} =
      (match overhang_length with
      | None -> ""
      | Some x ->
        sprintf "--sjdbOverhang %d" x
      ) ::
      (match sam_mapq_unique with
      | None -> ""
      | Some x ->
        if 0 > x || x > 255
        then failwith "STAR Align sam_mapq_unique must be between 0 and 255"
        else ();
        sprintf "--outSAMmapqUnique %d" x) ::
      List.concat_map parameters ~f:(fun (a, b) -> [a; b])
  end
end