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