Run: command-line choice of methods

lib/run.ml

@@ -120,15 +120,9 @@ type t = {
   tree_file : string ;
   alignment_dir : string ;
   convergent_species_file : string ;
-  use_tdg09 : bool ;
+  detection_methods : detection_method list ;
 }
 
-let detection_methods run =
-  List.filter_opt [
-    Some multinomial_method ;
-    if run.use_tdg09 then Some tdg09_method else None ;
-  ]
-
 let convergent_species_workflow run =
   [%workflow
     In_channel.read_lines
@@ -148,7 +142,6 @@ let dataset run =
   Dataset.make ~tree ~nucleotide_alignments ~convergent_species
 
 let repo run =
-  let detection_methods = detection_methods run in
   let d = dataset run in
   let foreach_detection_method (Detection_method meth as dm) =
     let report = candidate_site_report d dm in
@@ -160,25 +153,49 @@ let repo run =
       (Pipeline.alignment_plot q)
   in
   List.concat [
-    List.map detection_methods ~f:foreach_detection_method ;
+    List.map run.detection_methods ~f:foreach_detection_method ;
     List.map (Dataset.queries d) ~f:foreach_query ;
   ]
 
+let known_methods = [
+  "multinomial", multinomial_method ;
+  "tdg09", tdg09_method ;
+]
+
+let parse_methods methods =
+  List.map methods ~f:(fun m ->
+      match List.Assoc.find known_methods ~equal:String.equal m with
+      | Some dm -> Ok dm
+      | None ->
+        Rresult.R.error_msgf "Unknown method %s, known methods are %s"
+          m (List.map known_methods ~f:fst |> String.concat ~sep:",")
+    )
+  |> Result.all
+
 let main
     ~tree_file ~alignment_dir ~convergent_species_file
     ~outdir ~np ~mem
-    ~use_tdg09 () =
-
-  let loggers = [
-    Console_logger.create () ;
-  ] in
-  let mem = Option.map mem ~f:(fun i -> `GB i) in
-  let run = {
-    tree_file ; alignment_dir ; convergent_species_file ;
-    use_tdg09
-  } in
-  let repo = repo run in
-  Bistro_utils.Repo.build_main ~outdir ~loggers ?np ?mem repo
+    ~methods () =
+  try
+    let loggers = [
+      Console_logger.create () ;
+    ] in
+    let mem = Option.map mem ~f:(fun i -> `GB i) in
+    let detection_methods =
+      parse_methods methods
+      |> Rresult.R.failwith_error_msg
+    in
+    let run = {
+      tree_file ; alignment_dir ; convergent_species_file ;
+      detection_methods ;
+    } in
+    let repo = repo run in
+    Bistro_utils.Repo.build_main ~outdir ~loggers ?np ?mem repo
+  with
+  | Failure msg -> (
+      Stdlib.prerr_endline msg ;
+      exit 1
+    )
 
 let command =
   let open Command.Let_syntax in
@@ -197,10 +214,10 @@ let command =
         flag "--np" (optional int) ~doc:"INT Number of available processors"
       and mem =
         flag "--mem" (optional int) ~doc:"INT Available memory (in GB)"
-      and use_tdg09 =
-        flag "--tdg09" no_arg ~doc:" Use TDG09 method"
+      and methods =
+        flag "--methods" (optional_with_default [] (Command.Arg_type.comma_separated string)) ~doc:"STRING_LIST List of methods to be used"
       in
       main
         ~tree_file ~alignment_dir ~convergent_species_file ~outdir ~np ~mem
-        ~use_tdg09
+        ~methods
     ]