app/Reviewphiltrans: added use_diffsel option

app/reviewphiltrans_app.ml

@@ -5,14 +5,21 @@ let first_nhx_in_dir dir =
   Sys.readdir dir
   |> Array.find_exn ~f:(String.is_suffix ~suffix:".nhx")
 
-let realdata_main ~indir ~outdir ~np ~mem () =
+let sw b x = if b then Some x else None
+
+let realdata_main ~use_diffsel ~indir ~outdir ~np ~mem () =
   let mem = Option.map mem ~f:(fun i -> `GB i) in
   let rd =
     Real_dataset.make
       ~alignment_dir_path:(Filename.concat indir "Alignments")
       ~tree_path:(Filename.concat indir (first_nhx_in_dir indir))
   in
-  Real_dataset.repo [`Multinomial] rd
+  let meths = List.filter_opt [
+      sw use_diffsel `Diffsel ;
+      Some `Multinomial ;
+    ]
+  in
+  Real_dataset.repo meths rd
   |> Bistro_utils.Repo.build_main ~outdir ?np ?mem
 
 let realdata_command =
@@ -24,6 +31,8 @@ let realdata_command =
         flag "--outdir" (required string) ~doc:"PATH Output directory"
       and indir =
         flag "--indir" (required string) ~doc:"PATH Input directory"
+      and use_diffsel =
+        flag "--diffsel" no_arg ~doc:" use the diffsel method (very slow)."
       (* and preview =
        *   flag "--preview-mode" no_arg ~doc:" Preview mode"
        * and use_diffsel =
@@ -37,13 +46,13 @@ let realdata_command =
       and mem =
         flag "--mem" (optional int) ~doc:"INT Available memory (in GB)"
       in
-      realdata_main ~indir ~outdir ~np ~mem
+      realdata_main ~use_diffsel ~indir ~outdir ~np ~mem
     ]
 
 let () =
   Command.group ~summary:"Reviewphiltrans" [
     "validation", Pipeline.validation_command ;
-    "realdata", Pipeline.realdata_command ;
+    "realdata", realdata_command ;
     "alistats", Alistats.command ;
   ]
   |> Command.run