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 =
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
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