(Bfx : Semantics.Bioinformatics_base) = struct

  

(** This functions guesses whether to use fastq or fastq_gz given the file name extension. If r1 and r2 dot match, it fails with an exception. *)


  let fastq_of_files  ~sample_name ?fragment_id ~r1 ?r2 () =
    let is_gz r =
      Filename.check_suffix r1 ".gz" || Filename.check_suffix r1 ".fqz"
    in
    match is_gz r1, is_gz r2 with
    | true, true ->
      Bfx.(fastq_gz ~sample_name ?fragment_id ~r1 ?r2 () |> gunzip)
    | false, false ->
      Bfx.(fastq ~sample_name ?fragment_id ~r1 ?r2 ())
    | _ ->
      failwithf "fastq_of_files: cannot handle mixed gzipped and non-gzipped fastq pairs (for a given same fragment)"



(** Transform a value of type Input.t into a pipeline returning FASTQ data, providing the necessary intermediary steps. *)


  let fastq_of_input u =
    let open Input in
    match u with
    | Fastq {sample_name; files} ->
      List.map files ~f:(fun (fragment_id, source) ->
          match source with
          | PE (r1, r2) ->
            fastq_of_files ~sample_name ?fragment_id ~r1 ~r2 ()
          | SE r ->
            fastq_of_files ~sample_name ?fragment_id ~r1:r  ()
          | Of_bam (how, sorting, reference_build, path) ->
            let bam = Bfx.bam ~path ?sorting ~reference_build () in
            Bfx.bam_to_fastq ~sample_name ?fragment_id how bam
        )
      |> Bfx.list


end