Commit 603a2404 authored by Philippe Veber's avatar Philippe Veber
Browse files

app/Reviewphiltrans: added use_diffsel option

parent ee7d3395
...@@ -5,14 +5,21 @@ let first_nhx_in_dir dir = ...@@ -5,14 +5,21 @@ let first_nhx_in_dir dir =
Sys.readdir dir Sys.readdir dir
|> Array.find_exn ~f:(String.is_suffix ~suffix:".nhx") |> 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 mem = Option.map mem ~f:(fun i -> `GB i) in
let rd = let rd =
Real_dataset.make Real_dataset.make
~alignment_dir_path:(Filename.concat indir "Alignments") ~alignment_dir_path:(Filename.concat indir "Alignments")
~tree_path:(Filename.concat indir (first_nhx_in_dir indir)) ~tree_path:(Filename.concat indir (first_nhx_in_dir indir))
in 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 |> Bistro_utils.Repo.build_main ~outdir ?np ?mem
let realdata_command = let realdata_command =
...@@ -24,6 +31,8 @@ let realdata_command = ...@@ -24,6 +31,8 @@ let realdata_command =
flag "--outdir" (required string) ~doc:"PATH Output directory" flag "--outdir" (required string) ~doc:"PATH Output directory"
and indir = and indir =
flag "--indir" (required string) ~doc:"PATH Input directory" flag "--indir" (required string) ~doc:"PATH Input directory"
and use_diffsel =
flag "--diffsel" no_arg ~doc:" use the diffsel method (very slow)."
(* and preview = (* and preview =
* flag "--preview-mode" no_arg ~doc:" Preview mode" * flag "--preview-mode" no_arg ~doc:" Preview mode"
* and use_diffsel = * and use_diffsel =
...@@ -37,13 +46,13 @@ let realdata_command = ...@@ -37,13 +46,13 @@ let realdata_command =
and mem = and mem =
flag "--mem" (optional int) ~doc:"INT Available memory (in GB)" flag "--mem" (optional int) ~doc:"INT Available memory (in GB)"
in in
realdata_main ~indir ~outdir ~np ~mem realdata_main ~use_diffsel ~indir ~outdir ~np ~mem
] ]
let () = let () =
Command.group ~summary:"Reviewphiltrans" [ Command.group ~summary:"Reviewphiltrans" [
"validation", Pipeline.validation_command ; "validation", Pipeline.validation_command ;
"realdata", Pipeline.realdata_command ; "realdata", realdata_command ;
"alistats", Alistats.command ; "alistats", Alistats.command ;
] ]
|> Command.run |> Command.run
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment