Biocaml 0.4-dev : Biocaml_bed

open Core.Std

open Biocaml_internal_utils



type item = string * int * int * Biocaml_table.Row.t

with sexp



type parsing_spec = [

| `enforce of Biocaml_table.Row.t_type

| `strings

]

with sexp



module Error = struct



 type parsing_base = [

  | `wrong_format of

    [ `column_number

    | `float_of_string of string

    | `int_of_string of string ] *

     Biocaml_table.Row.t_type * string

  | `wrong_number_of_columns of Biocaml_table.Row.t ]

 with sexp



 type parsing = [ `bed of parsing_base ]

 with sexp



 type t = parsing with sexp

end



let item_of_line ~how line =

 let separators = ['\t'; ' '] in

 let format, strict =

  let base = [| `type_string; `type_int; `type_int |] in

  match how with

  | `strings -> (base, false)

  | `enforce tt -> (Array.append base tt, true) in

 Biocaml_table.Row.of_line ~separators ~format

  ~strict_row_length:strict ~strict_cell_type:strict line

 |> begin function

 | Ok row when Array.length row >= 3 ->

  let n = match row.(0) with `string s -> s | _ -> assert false in

  let h = match row.(1) with `int i -> i | _ -> assert false in

  let l = match row.(2) with `int i -> i | _ -> assert false in

  let q = Array.slice row 3 (Array.length row) in

  Ok (n, h, l, q)

 | Ok row ->

  Error (`bed (`wrong_number_of_columns row))

 | Error e -> Error (`bed e)

 end



let item_to_line (n, l, h, r) =

 Biocaml_table.Row.to_line ~sep:"\t"

  (Array.append [| `string n; `int l; `int h |] r)





module Transform = struct



 let string_to_item ?(more_columns=`strings) () =

  Biocaml_transform.on_output

   (Biocaml_lines.Transform.string_to_item ())

   ~f:(fun line -> item_of_line more_columns line)



 let item_to_string () =

  Biocaml_transform.on_input

   (Biocaml_lines.Transform.item_to_string ())

   ~f:(fun item -> item_to_line item)



end



exception Error of Error.t

let error_to_exn e = Error e



let in_channel_to_item_stream ?(buffer_size=65536) ?more_columns inp =

 let x = Transform.string_to_item ?more_columns () in

 Biocaml_transform.(in_channel_strings_to_stream inp x ~buffer_size)



let in_channel_to_item_stream_exn ?buffer_size ?more_columns inp =

 Stream.result_to_exn ~error_to_exn

  (in_channel_to_item_stream ?buffer_size ?more_columns inp)