let varscan_somatic ?adjust_mapq =
somatic_vc "varscan_somatic"
(fun () ->
sprintf "Amq%s"
(Option.value_map adjust_mapq ~default:"N" ~f:Int.to_string))
(fun () ->
`Assoc [
"adjust-mapq",
Option.value_map adjust_mapq
~default:(`String "None") ~f:(fun i -> `Int i)
])
()
(fun
~configuration ~run_with
~normal ~tumor ~result_prefix ->
Tools.Varscan.somatic_map_reduce ?adjust_mapq
~run_with ~normal ~tumor ~result_prefix ())
~configuration:()