diff --git a/flower.cabal b/flower.cabal
--- a/flower.cabal
+++ b/flower.cabal
@@ -1,5 +1,5 @@
 Name:           flower
-Version:        0.6.5
+Version:        0.7
 License:        GPL
 Cabal-Version:  >= 1.6
 Author:         Ketil Malde
@@ -22,10 +22,11 @@
                 invalid region.  This was likely a one-time bug in the 454 software, so this program
                 is probably not so useful any more.
 
-HomePage:       http://blog.malde.org/index.php/flower/
+HomePage:       http://biohaskell.org/Applications/Flower
 -- Source-Repository: http//malde.org/~ketil/biohaskell/flower
 Build-Type:     Simple
 Tested-with:    GHC==6.8.3, GHC==6.12.1
+Extra-Source-Files:  test.sh
 
 -- Data-files:     README
 Executable     flower
@@ -33,23 +34,26 @@
     Other-Modules:  Print, Metrics, Options, Fork
     Hs-Source-Dirs: src
     Ghc-Options:    -Wall -threaded
-    Build-Depends:  bio >= 0.4.8, base >=3 && <5, array >= 0.1, bytestring >= 0.9.1, binary == 0.4.*, random, cmdargs >= 0.5, containers, mtl
+    Build-Depends:  bio >= 0.4.9, base >=3 && <5, array >= 0.1, bytestring >= 0.9.1, binary == 0.4.*, random, cmdargs >= 0.5, containers, mtl
 
 Executable     flowselect
     Main-Is:        FlowSelect.hs
     Other-Modules:  Metrics
     Hs-Source-Dirs: src
     Ghc-Options:    -Wall
+    Build-Depends:  bio >= 0.4.9, random, base >= 3 && < 5
     Extensions:     ExistentialQuantification
 
 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
 
 Executable     flowt
@@ -59,4 +63,5 @@
       Ghc-Options:     -Wall -fno-warn-unused-do-bind
     else
       Ghc-Options:     -Wall
+    Build-Depends:  bio >= 0.4.9, base >= 3 && < 5, cmdargs >= 0.5, containers, bytestring >= 0.9.1
     Extensions:     DeriveDataTypeable
diff --git a/src/Flower.hs b/src/Flower.hs
--- a/src/Flower.hs
+++ b/src/Flower.hs
@@ -1,10 +1,11 @@
 -- FlowEr - FLOWgram ExtractoR
-
 module Main (main) where
 
 import Bio.Sequence.SFF
+import Bio.Sequence.SFF_filters
 import Bio.Sequence.Fasta
 import Bio.Sequence.FastQ (hWriteSangerQ,hWriteIllumina)
+import Bio.Sequence.SeqData (seqdata)
 -- import Bio.Util (countIO)
 
 import Print
@@ -54,7 +55,8 @@
       on (O.text o)      (\h -> mapM_ (hPutStrLn h . dumpText . tr . rs) =<< inp)
       on (O.fastq o)     (\h -> mapM_ (hWriteSangerQ h . map rbToSequence . tr . rs) =<< inp)
       on (O.illumina o)  (\h -> mapM_ (hWriteIllumina h . map rbToSequence . tr . rs) =<< inp)
-      on (O.summarize o) (\h -> mapM_ (L1.hPut h . summarize . tr . rs) =<< inp)
+      on (O.summarize o) (\h -> mapM_ (L1.hPut h . summarize . tr . rs) =<< inp)  -- should we trim?
+      on (O.filters o)   (\h -> mapM_ (L1.hPut h . sum_filters . rs) =<< inp)
       on (O.histogram o) (\h -> mapM_ (\(SFF c r) -> hPutStrLn h . showHist . histogram (B.unpack $ flow c) . map flowgram . tr $ r) =<< inp)
       on (O.flowgram o)  (\h -> mapM_ (\(SFF c r) -> L1.hPut h . L1.fromChunks . intersperse (B.pack "\n") . concatMap (showread c) $ r) =<< inp)
 
@@ -69,7 +71,7 @@
 mkTrimmer :: Opts -> Trimmer
 mkTrimmer o = case (O.trimKey o, O.trim o) of
         (True,True) -> error "Please specify only one of --trim and --trimkey"
-        (True,False) -> \r -> trimFromTo 4 (num_bases $ read_header r) r
+        (True,False) -> \r -> trimFromTo 5 (num_bases $ read_header r) r
         (False,True) -> trim
         (False,False) -> id
 
@@ -86,7 +88,7 @@
                           , clip,     show (clip_qual_left rh), sp, show (clip_qual_right rh), nl
                           , flows,    B.unpack $ B.unwords $ map fi $ flowgram r, nl
                           , idx,      unwords $ map show $ cumulative_index' r, nl
-                          , base,     L.unpack (masked_bases' r), nl
+                          , base,     L.unpack (seqdata . rbToSequence $ r), nl
                           , qual,     unwords $ map show $ L1.unpack (quality r), nl
                              ]
           where rh = read_header r
@@ -103,18 +105,6 @@
                 formatRN (ReadName (yr,mo,dy) (h,m,s) r' x y) = 
                   printf "%4d-%02d-%02d %02d:%02d:%02d R%d (%d,%d)" yr mo dy h m s r' x y
 
-
--- Get the bases, but lower case masked bases.  Also in biolib's SFF.hs (sans prime),
--- so this is only for backwards compatibility with biolib <= 0.4.6.
-masked_bases' :: ReadBlock -> SeqData
-masked_bases' rb = let
-  l = fromIntegral $ clip_qual_left $ read_header rb
-  r = fromIntegral $ clip_qual_right $ read_header rb
-  s = bases rb
-  in L.concat [ L.map toLower $ L.take (l-1) s
-              , L.take r (L.drop (l-1) s)
-              , L.map toLower $ L.drop r s]
-
 cumulative_index' :: ReadBlock -> [Int]
 cumulative_index' = scanl1 (+) . map fromIntegral . B1.unpack . flow_index
 
@@ -133,7 +123,7 @@
 -- ----------------------------------------------------------
 
 -- | Summarize each read on one line of output
-summarize :: [ReadBlock] -> L1.ByteString
+summarize :: [ReadBlock] -> L.ByteString
 summarize rs = do
   L.concat [ L.pack "# name........\tdate......\ttime....\treg\ttrim_l\ttrim_r\tx_loc\ty_loc\tlen\tK2\ttrimK2\tncount\tavgQ\ttravgQ\n"
            , toLazyByteString . mconcat . map sum1 $ rs]
@@ -163,6 +153,25 @@
                         , fromByteString (fi $ quals $ flowgram r), fromByteString (fi $ quals $ flowgram tr)
                         , putInt (n_count r)
                         , avg_qual $ quality r, avg_qual $ quality tr]) ++ [nl]
+
+-- ----------------------------------------------------------
+-- The --filters option, summarize filters
+-- ----------------------------------------------------------
+sum_filters ::  [ReadBlock] -> L1.ByteString
+sum_filters rs = toLazyByteString $ mconcat (header:map sumf1 rs)
+  where 
+    header = fromByteString $ B.pack "# name..... \tlength \tl_trim \tr_trim \tE K D M L\tSig Q20 Adp\n"
+    sumf1 rb = let
+      rh = read_header rb
+      rn = read_name rh
+      nb = fromIntegral $ num_bases rh
+      (cl,cr) = (fromIntegral $ clip_qual_left rh, fromIntegral $ clip_qual_right rh)
+      dfs = mconcat $ intersperse (char ' ') $
+            map (\f -> if f rb then char '+' else char ' ') 
+            [discard_empty, discard_key "tcag", discard_dots 0.05, discard_mixed, discard_length 186]
+      tfs = mconcat $ intersperse (char ' ') $ map (\f -> putInt3 (f rb))
+            [sigint, qual20 10, find_primer rapid_adapter]
+      in mconcat (intersperse (char '\t') [fromByteString rn, putInt nb, putInt cl, putInt cr, dfs, tfs]++[char '\n'])
 
 -- ----------------------------------------------------------
 -- The -F option: Output the sequence of flows, one flow per line
diff --git a/src/Flowt.hs b/src/Flowt.hs
--- a/src/Flowt.hs
+++ b/src/Flowt.hs
@@ -30,7 +30,7 @@
 splitRes (EndWith e) = ([],e)
 
 trim :: ReadBlock -> ReadBlock
-trim = id -- trimFromTo 4 10000 <- this trims to last base called position!
+trim = id -- trimFromTo 4 10000 <- this trims to last base called position! (use trimKey?)
 
 data Options = O { thresh :: Double
                  , fplen  :: Int
@@ -46,7 +46,7 @@
            , clusters  = True &= help "output complete clusters"
            , input  = def  &= args &= typFile }
          &= program "flowt"
-         &= summary "flowt v0.6 - filter out reads from duplicate clones in 454 sequencing."
+         &= summary "flowt v0.7 - filter out reads from duplicate clones in 454 sequencing."
 
 vlog :: Bool -> String -> IO ()
 vlog v s = when v (hPutStr stderr s >> hFlush stderr)
diff --git a/src/Options.hs b/src/Options.hs
--- a/src/Options.hs
+++ b/src/Options.hs
@@ -10,6 +10,7 @@
             { trimKey :: Bool
             , trim    :: Bool
             , summarize :: Maybe FilePath
+            , filters :: Maybe FilePath
             , info    :: Maybe FilePath
             , fasta   :: Maybe FilePath
             , fqual  :: Maybe FilePath
@@ -29,6 +30,7 @@
   { trimKey = False &= help "Trim only the TCAG key sequence"
   , trim    = False &= help "Trim quality using clipping information"     &= name "t"
   , summarize = def   &= help "Output per sequence summary information"   &= typFile &= optdef
+  , filters   = def   &= help "Output filtering information"              &= typFile &= optdef
   , info    = def   &= help "Output brief overview of the contents"       &= typFile &= optdef
   , fasta   = def   &= help "Output FASTA-formatted sequences"            &= typFile &= name "f" &= optdef
   , fqual    = def   &= help "Output phred qualities"                      &= typFile &= name "q" &= optdef
@@ -39,14 +41,14 @@
   , text      = def &= help "Output SFF information as text (default)"    &= typFile &= name "T" &= optdef
   , inputs  = def &= args &= typFile
   } 
-  &= summary "flower v0.6.5 - Extract information from SFF files" 
+  &= summary "flower v0.7 - Extract information from SFF files" 
   &= program "flower"
 
 getArgs :: IO Opts
 getArgs = do
   o <- cmdArgs opts 
   -- print o
-  let outs = filter isJust $ map ($o) [summarize,info,fasta,fqual,fastq,illumina,flowgram,histogram,text]
+  let outs = filter isJust $ map ($o) [summarize,filters,info,fasta,fqual,fastq,illumina,flowgram,histogram,text]
   when ((length $ filter (==Just "-") $ outs) > 1) $ error "If you specify more than one output format, you need to specify output files"
   let o' = if null outs then o { text = Just "-" } else o
   return o'
diff --git a/src/Print.hs b/src/Print.hs
--- a/src/Print.hs
+++ b/src/Print.hs
@@ -1,7 +1,7 @@
 module Print 
     (
      Builder, toLazyByteString, mconcat, fromByteString, char
-    , putInt, putInt2, putDate, putTime, putFix
+    , putInt, putInt2, putInt3, putDate, putTime, putFix
     ) where 
 
 import Data.Binary.Builder
@@ -23,15 +23,17 @@
 -- zero padded ints
 
 putInt2 :: Int -> Builder
-putInt2 x = fromByteString (int2s!x)
+putInt2 x | x<100 = fromByteString (int2s!x)
+          | otherwise = fromByteString (pack "xx")
 
 putInt3 :: Int -> Builder
-putInt3 x = fromByteString (int3s!x)
+putInt3 x | x<1000 = fromByteString (int3s!x)
+          | otherwise = fromByteString (pack "xxx")
 
 ints, int2s, int3s :: Array Int ByteString
 ints  = listArray (0,999) [pack (show i) | i <- [0..999::Int]]
 int2s = listArray (0,99) (map (pack . ('0':) . show) [0..9::Int]++[pack (show i) | i <- [10..99::Int]])
-int3s = listArray (0,999) (map (pack . ('0':) . ('0':) . show) [0..9::Int] ++ map (pack . ('0':) . show ) [10..99::Int] ++ map (pack . show) [100..999::Int])
+int3s = listArray (0,999) (map (pack . (' ':) . (' ':) . show) [0..9::Int] ++ map (pack . (' ':) . show ) [10..99::Int] ++ map (pack . show) [100..999::Int])
 
 putDate :: Int -> Int -> Int -> Builder
 putDate y m d = mconcat [putInt y, dash, putInt2 m, dash, putInt2 d]
diff --git a/test.sh b/test.sh
new file mode 100644
--- /dev/null
+++ b/test.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+#
+# This script downloads test data, and checks that flower produces consistent
+# output.
+get_data(){
+	wget http://malde.org/~ketil/test.sff
+	wget http://malde.org/~ketil/test.md5
+}
+
+cabal configure
+cabal build
+
+get_data
+
+# run tests:
+
+dist/build/flower/flower -f=test.fasta -q=test.qual -Q=test.fastq -T=test.txt test.sff
+md5sum test.{fasta,qual,fastq,txt} > new.md5
+
+diff -u test.md5 new.md5 && echo "Test succeessful" || echo "TEST FAILED"
+