add --no-hapc

lib/pipeline.ml

@@ -73,7 +73,7 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile_f ~
   let ready_dataset = { Ready_dataset.input_tree = input_tree ; tree_dataset ; fna; faa; fna_infos} in
   { Dataset.model_prefix; is_real= false; tree_prefix; dataset = ready_dataset }
 
-let derive_from_tree ~tree_dir ~tree ~profile_f ~preview ~use_concat ~ns ~no_Ne =
+let derive_from_tree ~tree_dir ~tree ~profile_f ~preview ~use_concat ~ns ~no_Ne ~no_HaPC =
   let tree_prefix = Filename.chop_extension tree in
   let input_tree = input (Filename.concat tree_dir tree) in
   let tree_dataset = Tree_dataset.prepare input_tree in
@@ -85,9 +85,16 @@ let derive_from_tree ~tree_dir ~tree ~profile_f ~preview ~use_concat ~ns ~no_Ne
       if preview then
         []
       else
-      if no_Ne then
+        [(
+          if no_HaPC then
+            []
+          else
             [HaPC           ;
             ]
+        )
+         ;
+         (if no_Ne then
+            []
           else
             [HaPC           ;
              H0_NeSmall      ;
@@ -97,6 +104,8 @@ let derive_from_tree ~tree_dir ~tree ~profile_f ~preview ~use_concat ~ns ~no_Ne
              HaPCOC_NeBig    ;
              HaPC_NeBig      ;
             ]
+         )
+        ] |> List.concat
     ] |> List.concat
   in
   let dataset_per_hypo = List.map models ~f:(fun model ->
@@ -108,10 +117,10 @@ let derive_from_tree ~tree_dir ~tree ~profile_f ~preview ~use_concat ~ns ~no_Ne
   let dataset_concat_hypos = if use_concat then [concat_H0Ha;] else [] in
   List.concat [ dataset_per_hypo ; dataset_concat_hypos ]
 
-let derive_sim ~tree_dir ~trees ~profile_fn ~preview ~use_concat ~ns ~no_Ne =
+let derive_sim ~tree_dir ~trees ~profile_fn ~preview ~use_concat ~ns ~no_Ne ~no_HaPC =
   let profile_f = input profile_fn in
   List.map trees ~f:(fun tree ->
-      derive_from_tree ~tree_dir ~tree ~profile_f ~preview ~use_concat ~ns ~no_Ne)
+      derive_from_tree ~tree_dir ~tree ~profile_f ~preview ~use_concat ~ns ~no_Ne ~no_HaPC)
   |> List.concat
 
 
@@ -245,20 +254,20 @@ let detection_main ~outdir ~indir ?(np = 2) ?(mem = 2) ~preview ~fast_mode () =
   let repo = repo_of_dataset_results_l ~dataset_results_l in
   Repo.build ~outdir ~np ~mem:(`GB mem) ~logger repo
 
-let simulation_main ~outdir ?(ns = 0) ?(np = 2) ?(mem = 2) ~tree_dir ~profile_fn ~preview ~use_concat ~no_Ne () =
+let simulation_main ~outdir ?(ns = 0) ?(np = 2) ?(mem = 2) ~tree_dir ~profile_fn ~preview ~use_concat ~no_Ne ~no_HaPC () =
   let trees = Array.to_list @@ Sys.readdir tree_dir in
-  let dataset_l = derive_sim ~tree_dir ~trees ~profile_fn ~preview ~use_concat ~ns ~no_Ne in
+  let dataset_l = derive_sim ~tree_dir ~trees ~profile_fn ~preview ~use_concat ~ns ~no_Ne ~no_HaPC in
   let repo = Dataset.repo dataset_l ~preview in
   Repo.build ~outdir ~np ~mem:(`GB mem) ~logger repo
 
-let validation_main ~outdir ?(indir = "") ?(ns = 0) ?(np = 2) ?(mem = 2) ~preview ~fast_mode ~no_Ne ~tree_dir ~profile_fn ~use_concat () =
+let validation_main ~outdir ?(indir = "") ?(ns = 0) ?(np = 2) ?(mem = 2) ~preview ~fast_mode ~no_Ne ~no_HaPC ~tree_dir ~profile_fn ~use_concat () =
   let trees = Array.to_list @@ Sys.readdir tree_dir in
   let repo = List.map trees ~f:(fun tree ->
       let trees = [tree] in
       let tree_prefix = Filename.chop_extension tree in
       let indir_dataset_l = if indir = "" then [] else parse_input_data indir in
       let dataset_l =
-        derive_sim ~tree_dir ~trees ~profile_fn ~preview ~use_concat ~ns ~no_Ne
+        derive_sim ~tree_dir ~trees ~profile_fn ~preview ~use_concat ~ns ~no_Ne ~no_HaPC
         @ indir_dataset_l in
       let dataset_results_l = derive_det ~dataset_l ~preview ~fast_mode in
       let post_analyses = Post_analyses.post_analyses_of_dataset_results_l ~dataset_results_l in
@@ -285,6 +294,8 @@ let simulation_command =
         flag "--preview-mode" no_arg ~doc:" Preview mode"
       and no_Ne =
         flag "--no-ne" no_arg ~doc:" mode without hypothesis including different Ne"
+      and no_HaPC =
+        flag "--no-hapc" no_arg ~doc:" mode without ~HaPC hypothesis"
       and ns =
         flag "--ns" (optional int) ~doc:"INT Number of sites to simulate"
       and np =
@@ -298,7 +309,7 @@ let simulation_command =
       and profile_fn =
         flag "--profile-fn" (required string) ~doc:"PATH Path to profile file"
       in
-      simulation_main ~outdir ?ns ?np ?mem ~no_Ne ~tree_dir ~profile_fn ~preview ~use_concat
+      simulation_main ~outdir ?ns ?np ?mem ~no_Ne ~no_HaPC ~tree_dir ~profile_fn ~preview ~use_concat
     ]
 
 let detection_command =
@@ -337,6 +348,8 @@ let validation_command =
         flag "--fast" no_arg ~doc:" 'Fast' mode without the most costly methods"
       and no_Ne =
         flag "--no-ne" no_arg ~doc:" mode without hypothesis including different Ne"
+      and no_HaPC =
+        flag "--no-hapc" no_arg ~doc:" mode without ~HaPC hypothesis"
       and use_concat =
         flag "--use-concat" no_arg ~doc:" Use concatenation H0+Ha_pcoc"
       and ns =
@@ -350,5 +363,5 @@ let validation_command =
       and profile_fn =
         flag "--profile-fn" (required string) ~doc:"PATH Path to profile file"
       in
-      validation_main ~outdir ?indir ?ns ?np ?mem ~preview ~fast_mode ~no_Ne ~tree_dir ~profile_fn ~use_concat
+      validation_main ~outdir ?indir ?ns ?np ?mem ~preview ~fast_mode ~no_Ne ~no_HaPC ~tree_dir ~profile_fn ~use_concat
     ]