struct
| (**************************************************************************) |
(* Copyright 2014, Sebastien Mondet <seb@mondet.org> *)
(* *)
(* Licensed under the Apache License, Version 2.0 (the "License"); *)
(* you may not use this file except in compliance with the License. *)
(* You may obtain a copy of the License at *)
(* *)
(* http://www.apache.org/licenses/LICENSE-2.0 *)
(* *)
(* Unless required by applicable law or agreed to in writing, software *)
(* distributed under the License is distributed on an "AS IS" BASIS, *)
(* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or *)
(* implied. See the License for the specific language governing *)
(* permissions and limitations under the License. *)
| (**************************************************************************) |
open Common
| (** Positions are 1-based *) |
type t = [
| `Chromosome of string
| `Chromosome_interval of string * int * int
| `Full
]
| (** Make a filename-compliant string out of a region specification. *) |
let to_filename = function
| `Full -> "Full"
| `Chromosome s -> sprintf "%s" s
| `Chromosome_interval (s, b, e) -> sprintf "%s_%d-%d" s b e
let to_samtools_specification = function
| `Full -> None
| `Chromosome s -> Some s
| `Chromosome_interval (s, b, e) -> Some (sprintf "%s:%d-%d" s b e)
let to_samtools_option r =
match to_samtools_specification r with
| Some s -> sprintf "-r %s" s
| None -> ""
let to_gatk_option r =
match to_samtools_specification r with
| Some s -> sprintf "--intervals %s" s
| None -> ""
let parse_samtools s =
match String.split ~on:(`Character ':') s with
| [] -> assert false
| [one] -> `Chromosome one
| [one; two] ->
begin match String.split ~on:(`Character '-') two with
| [left; right] ->
begin match Int.of_string left, Int.of_string right with
| Some b, Some e -> `Chromosome_interval (one, b, e)
| _ -> failwithf "Cannot parse %S into 2 loci" two
end
| _ -> failwithf "Not one '-' in %S" two
end
| _ -> failwithf "Not one or zero ':' in %S" s
let cmdliner_term () =
let open Cmdliner in
Term.(
pure (function
| None -> `Full
| Some s -> parse_samtools s)
$ Arg.(
value & opt (some string) None
& info ["R"; "region"] ~docv:"REGION"
~doc:"Specify a region; using samtools' format"
)
)
end