hunk ./flower.cabal 47
-Executable     frecover
-    Main-Is:        FRecover.hs
-    Hs-Source-Dirs: src
-    Build-Depends:  bio >= 0.4.9, base >= 3 && < 5
-    Ghc-Options:    -Wall
-
-Executable     frename
-    Main-Is:        FRename.hs
-    Hs-Source-Dirs: src
-    Build-Depends:  bio >= 0.4.9, base >= 3 && < 5, bytestring >= 0.9.1
-    Ghc-Options:    -Wall
-
hunk ./src/FRecover.hs 1
-
-module Main where
-import Bio.Sequence.SFF
-import System.Environment (getArgs)
-
-main :: IO ()
-main = mapM_ recoverFile =<< getArgs
-  where recoverFile f = writeSFF (f++"_recovered") =<< recoverSFF f
-
rmfile ./src/FRecover.hs
hunk ./src/FRename.hs 1
-
-{-|
-  Rename reads in .SFF files to avoid name clashes.
-  Apparently, reads with the same name crashes Newbler, and is
-  in any case a bad idea.  This ensures uniqueness by appending a serial number to each read name in a set of files.
--}
-
-module Main where
-
-import Bio.Sequence.SFF
-import System.Environment (getArgs)
-import qualified Data.ByteString.Char8 as B
-
-main :: IO ()
-main = do
-  fs <- getArgs
-  if null fs then putStrLn "Usage: frename file1.sff [file2.sff ...]"
-    else renameSFFs fs
-         
-renameSFFs :: [FilePath] -> IO ()
-renameSFFs = go 0 
-  where go _ [] = return ()
-        go current (f:fs) = do
-          (SFF h rs) <- readSFF f
-          writeSFF ("r_"++f) (SFF h $ renameFrom current rs)
-          go (current+num_reads h) fs
-        renameFrom i rs = zipWith update [i..] rs
-          where update j r = let h = read_header r
-                                 rn = B.concat [read_name h, B.pack "_", B.pack (show j)]
-                             in r { read_header = h { name_length = fromIntegral $ B.length rn, read_name = rn }}
rmfile ./src/FRename.hs
hunk ./flower.cabal 2
-Version:        0.7
+Version:        0.7.1
hunk ./flower.cabal 17
-                The fselect executable extracts reads from SFF-files, generating a new
-                SFF-file with a subset of the reads based on various criteria.
-                .
-                Sometimes SFF files will appear to be corrupted, with all-zero blocks in the
-                file. The frecover program ignores these and tries to resync with the file after an 
-                invalid region.  This was likely a one-time bug in the 454 software, so this program
-                is probably not so useful any more.
-
+                The flowselect executable extracts reads from SFF-files, generating a new
+                SFF-file with a subset of the reads based on various quality criteria.
+		.
+		The flowt program removes (artificial) duplicates from SFF files.  It's currently a work
+		in progress, but included if you'd like to play with it.  It's faster than other approaches 
+		(e.g. CD-HIT), and ought to be more sensitive and specific, but this needs to be proven.
hunk ./src/Print.hs 21
-             (a,r) -> putInt a `append` putInt3 r
+             (a,r) -> putInt a `append` putInt3_0 r
hunk ./src/Print.hs 33
-ints, int2s, int3s :: Array Int ByteString
+putInt3_0 :: Int -> Builder
+putInt3_0 x | x<1000 = fromByteString (int3s0!x)
+            | otherwise = fromByteString (pack "xxx")
+
+ints, int2s, int3s, int3s0 :: Array Int ByteString
hunk ./src/Print.hs 41
+int3s0 = listArray (0,999) (map (pack . ('0':) . ('0':) . show) [0..9::Int] ++ map (pack . ('0':) . show ) [10..99::Int] ++ map (pack . show) [100..999::Int])