struct

  
  (** Call a command on a list of ~vcfs to produce a given ~final_vcf (hence the n-to-1 naming). *)

  let vcf_process_n_to_1_no_machine
      ~host
      ~vcftools
      ~(run_program : Machine.Make_fun.t)
      ?(more_edges = [])
      ~vcfs
      ~final_vcf
      command_prefix
    =
    let open KEDSL in
    let name = sprintf "%s-%s" command_prefix (Filename.basename final_vcf) in
    let make =
      run_program ~name
        Program.(
          Machine.Tool.(init vcftools)
          && shf "%s %s > %s"
            command_prefix
            (String.concat ~sep:" "
               (List.map vcfs ~f:(fun t -> Filename.quote t#product#path)))
            final_vcf
        ) in
    workflow_node ~name
      (single_file final_vcf ~host)
      ~make
      ~edges:(
        on_failure_activate
          (Remove.path_on_host ~host final_vcf)
        :: depends_on Machine.Tool.(ensure vcftools)
        :: List.map ~f:depends_on vcfs
        @ more_edges)

  
  (** Concatenate VCF files.

We use this version where we don't yet have a Machine.t, as in "download_reference_genome.ml". *)


  let vcf_concat_no_machine
      ~host
      ~vcftools
      ~(run_program : Machine.Make_fun.t)
      ?more_edges
      vcfs
      ~final_vcf =
    vcf_process_n_to_1_no_machine
      ~host ~vcftools ~run_program ?more_edges ~vcfs ~final_vcf
      "vcf-concat"

  
  (** Sort a VCF file by choromosome position (it uses "vcf-sort" which itself relies on the "sort" unix tool having the "--version-sort" option).

We use this version where we don't yet have a Machine.t, as in "download_reference_genome.ml". *)


  let vcf_sort_no_machine
      ~host
      ~vcftools
      ~(run_program : Machine.Make_fun.t)
      ?more_edges
      ~src ~dest () =
    let run_program =
      Machine.Make_fun.with_requirements run_program [`Memory `Big] in 
    vcf_process_n_to_1_no_machine
      ~host ~vcftools ~run_program ?more_edges ~vcfs:[src] ~final_vcf:dest
      "vcf-sort -c"

end