biosff 0.3.7 → 0.3.7.1

raw patch · 4 files changed

+43/−3 lines, 4 files

Files

• biosff.cabal +2/−1
• src/FClip/Options.hs +35/−0
• src/FRecover/Main.hs +5/−1
• src/Flower/Options.hs +1/−1

@@ -1,5 +1,5 @@ Name:                biosff-Version:             0.3.7+Version:             0.3.7.1 Synopsis:            Library and executables for working with SFF files Description:         The library contains the functionality for reading and writing 		     SFF files (sequencing data from 454 and Ion Torrent).  It duplicates@@ -65,6 +65,7 @@  Executable fclip   Main-Is:         Main.hs+  Other-Modules:   Options   if flag(fclip)      Buildable:  True   else

@@ -0,0 +1,35 @@+{-# LANGUAGE DeriveDataTypeable #-}++module Options where++import System.Console.CmdArgs++data Opts = Opts +            { trimKey :: Bool+            , trimAdapter :: Bool+            , trim    :: Bool+            , filterEmpty :: Bool+            , output :: FilePath+            , input  :: FilePath+            } deriving (Data,Typeable, Show, Eq)++opts :: Opts+opts = Opts+  { trimKey = False &= help "Trim only the TCAG key sequence"             &= name "k"+  , trim    = False &= help "Trim quality using clipping information"     &= name "t"+  , trimAdapter = False &= help "Trim quality using adapter information"  &= name "a"+  , filterEmpty = False &= help "Filter out reads that are empty after trimming" &= name "E"+  , output = def &= help "SFF file to write" &= name "o"+  , input  = def &= args &= typFile+  } +  &= summary "fclip (biosff v0.3.7.1) - Extract information from SFF files" +  &= program "fclip"++getArgs :: IO Opts+getArgs = do+  o <- cmdArgs opts +  -- todo: option checking+  return o++            +            

@@ -7,7 +7,11 @@ import System.Environment (getArgs)  main :: IO ()-main = mapM_ recoverFile =<< getArgs+main = do +  xs <- getArgs+  if null xs +    then error "frecover (biosff 0.3.7.1) - try to repair broken SFF files.\nUsage: frecover file.sff [file.sff]" +    else do mapM_ recoverFile xs   where recoverFile f = writeSFF (f++"_recovered") =<< recoverSFF f   -- perhaps we should use writeSFF' instead, since it goes back   -- to update the header with number of reads written?

@@ -47,7 +47,7 @@   , text      = def &= help "Output SFF information as text (default)"    &= typFile &= name "T" &= optdef   , inputs  = def &= args &= typFile   } -  &= summary "flower (biosff v0.3.7) - Extract information from SFF files" +  &= summary "flower (biosff v0.3.7.1) - Extract information from SFF files"    &= program "flower"  getArgs :: IO Opts