From dd38d0d1dda2be42bf280aeca110542f2f2fef1b Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Tue, 28 May 2013 10:47:11 -0400
Subject: removed files

---
 src/nbc/count.ml | 60 --------------------------------------------------------
 1 file changed, 60 deletions(-)
 delete mode 100644 src/nbc/count.ml

(limited to 'src/nbc/count.ml')

diff --git a/src/nbc/count.ml b/src/nbc/count.ml
deleted file mode 100644
index bd97b7b..0000000
--- a/src/nbc/count.ml
+++ /dev/null
@@ -1,60 +0,0 @@
-module ExtArray = ExtArray.Array
-let (|>) a b = b a
-
-module Options = struct
-	let parser = OptParse.OptParser.make ~version:"1.0" ()
-	let per_word =
-		let option = OptParse.StdOpt.str_option ~metavar:"file" () in
-		OptParse.OptParser.add parser ~short_name:'w' ~long_name:"per-word"
-			~help:"file to store per-word counts in" option;
-		(fun () -> match OptParse.Opt.opt option with
-			Some x -> x
-			| None ->
-				OptParse.OptParser.usage parser ();
-				exit 1
-		)
-	let total =
-		let option = OptParse.StdOpt.str_option ~metavar:"file" () in
-		OptParse.OptParser.add parser ~short_name:'t' ~long_name:"total"
-			~help:"file to store total count in" option;
-		(fun () -> match OptParse.Opt.opt option with
-			Some x -> x
-			| None ->
-				OptParse.OptParser.usage parser ();
-				exit 1
-		)
-	let order =
-		let option = OptParse.StdOpt.int_option ~default:15 () in
-		OptParse.OptParser.add parser ~short_name:'r' ~long_name:"order" option;
-		(fun () -> OptParse.Opt.get option)
-	let files = OptParse.OptParser.parse_argv parser
-	let total = total ()
-	let per_word = per_word ()
-	let order = order ()
-end
-
-let load_file order judy total name =
-	Misc.io_of_gzip name |> Fasta.enum_words order
-	|> Enum.fold (fun word total ->
-		Judy.bump judy word;
-		Judy.bump judy (Gene.reverse word);
-		total + 2
-	) total
-let load_files order names =
-	let judy = Judy.create () in
-	List.fold_left (load_file order judy) 0 names, judy
-let gzip_output_string c s = Gzip.output c s 0 (String.length s)
-let () =
-	let total_words, judy = load_files Options.order Options.files in
-	(
-		let c = open_out Options.total in
-		output_string c (string_of_int total_words ^ "\n");
-		close_out c
-	); (
-		let c = Gzip.open_out Options.per_word in
-		Judy.iter (fun word count ->
-			gzip_output_string c
-				(String.concat "" [string_of_int count; " "; word; "\n"])
-		) judy;
-		Gzip.close_out c
-	)
-- 
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