reviewphiltrans_app: add options for pcoc* diffsel identical topological + a logger

app/reviewphiltrans_app.ml

 open Core
 open Reviewphiltrans
+open Bistro_utils
+
 
 let first_nhx_in_dir dir =
   Sys.readdir dir
@@ -7,20 +9,36 @@ let first_nhx_in_dir dir =
 
 let sw b x = if b then Some x else None
 
-let realdata_main ~use_diffsel ~indir ~outdir ~np ~mem () =
+let realdata_main ~use_diffsel
+                  ~use_pcoc
+                  ~use_pcoc_c60
+                  ~use_pcoc_gamma
+                  ~use_topological
+                  ~use_identical
+                  ~no_use_multinomial
+                  ~indir ~outdir ~np ~mem () =
+  let loggers = [
+      Console_logger.create () ;
+  ] in
   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
+  let use_multinomial = not no_use_multinomial in
   let meths = List.filter_opt [
       sw use_diffsel `Diffsel ;
-      Some `Multinomial ;
+      sw use_pcoc `Pcoc ;
+      sw use_pcoc_c60 `Pcoc_c60 ;
+      sw use_pcoc_gamma `Pcoc_gamma ;
+      sw use_topological `Topological ;
+      sw use_identical `Identical ;
+      sw use_multinomial `Multinomial ;
     ]
   in
   Real_dataset.repo meths rd
-  |> Bistro_utils.Repo.build_main ~outdir ?np ?mem
+  |> Bistro_utils.Repo.build_main ~outdir ~loggers ?np ?mem
 
 let realdata_command =
   let open Command.Let_syntax in
@@ -33,20 +51,35 @@ let realdata_command =
         flag "--indir" (required string) ~doc:"PATH Input directory"
       and use_diffsel =
         flag "--diffsel" no_arg ~doc:" use the diffsel method (very slow)."
+      and use_pcoc =
+        flag "--pcoc" no_arg ~doc:" use the pcoc method (slow)."
+      and use_pcoc_c60 =
+        flag "--pcoc_c60" no_arg ~doc:" use the pcoc method with c60 profils (very_slow)."
+      and use_pcoc_gamma =
+        flag "--pcoc_gamma" no_arg ~doc:" use the pcoc method with the gamma option (very_slow)."
+      and use_topological =
+        flag "--topological" no_arg ~doc:" use the topological method (fast)."
+      and use_identical =
+        flag "--identical" no_arg ~doc:" use the identical method (fast)."
+      and no_use_multinomial =
+        flag "--no-multinomial" no_arg ~doc:" not use the multinomial method (very fast so by default)."
       (* and preview =
        *   flag "--preview-mode" no_arg ~doc:" Preview mode"
-       * and use_diffsel =
-       *   flag "--diffsel" no_arg ~doc:" use the diffsel method (very slow)."
-       * and use_c60 =
-       *   flag "--c60" no_arg ~doc:" use the pcoc c60 method (slow)."
        * and calc_dnds =
-       *   flag "--dnds" no_arg ~doc:" calculate dn ds dnds trees (slow)." *)
+       *   flag "--dnds" no_arg ~doc:" calculate dn ds dnds trees (slow)."*)
       and np =
         flag "--np" (optional int) ~doc:"INT Number of available processors"
       and mem =
         flag "--mem" (optional int) ~doc:"INT Available memory (in GB)"
       in
-      realdata_main ~use_diffsel ~indir ~outdir ~np ~mem
+      realdata_main ~use_diffsel
+                    ~use_pcoc
+                    ~use_pcoc_c60
+                    ~use_pcoc_gamma
+                    ~use_topological
+                    ~use_identical
+                    ~no_use_multinomial
+                    ~indir ~outdir ~np ~mem
     ]
 
 let () =