flower 0.6.3 → 0.6.5
raw patch · 3 files changed
+11/−8 lines, 3 files
Files
- flower.cabal +5/−2
- src/Flower.hs +5/−5
- src/Options.hs +1/−1
flower.cabal view
@@ -1,5 +1,5 @@ Name: flower-Version: 0.6.3+Version: 0.6.5 License: GPL Cabal-Version: >= 1.6 Author: Ketil Malde@@ -55,5 +55,8 @@ Executable flowt Main-Is: Flowt.hs Hs-Source-Dirs: src- Ghc-Options: -Wall -fno-warn-unused-do-bind+ if impl(ghc >= 6.12)+ Ghc-Options: -Wall -fno-warn-unused-do-bind+ else+ Ghc-Options: -Wall Extensions: DeriveDataTypeable
src/Flower.hs view
@@ -35,7 +35,7 @@ main :: IO () main = do opts <- O.getArgs- when (null $ O.inputs opts) $ error "Please provide an input file!"+ when (null $ O.inputs opts) $ error "Please provide an input file - or use --help for more information." forkAndWait $ buildActions opts type Action = IO ()@@ -53,7 +53,7 @@ on (O.fqual o) (\h -> mapM_ (hWriteQual h . map rbToSequence . tr . rs) =<< inp) 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.fastq o) (\h -> mapM_ (hWriteIllumina 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.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)@@ -84,7 +84,7 @@ , let (lf,rt) = (clip_adapter_right rh, clip_adapter_left rh) in if lf /= 0 || rt /= 0 then adapter ++ show lf ++ sp++ show rt else "" , clip, show (clip_qual_left rh), sp, show (clip_qual_right rh), nl- , flows, unwords $ map show $ flowgram r, 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 , qual, unwords $ map show $ L1.unpack (quality r), nl@@ -165,7 +165,7 @@ , avg_qual $ quality r, avg_qual $ quality tr]) ++ [nl] -- ------------------------------------------------------------- The -f option: Output the sequence of flows, one flow per line+-- The -F option: Output the sequence of flows, one flow per line -- ---------------------------------------------------------- fi :: Flow -> ByteString@@ -210,7 +210,7 @@ qgroup _ _ = error "internal error in 'qgroup'" -- ------------------------------------------------------------- The -h and -H options: Output a histogram of flow values+-- The -h option: Output a histogram of flow values -- ---------------------------------------------------------- type Hist = UArray Flow Int
src/Options.hs view
@@ -39,7 +39,7 @@ , text = def &= help "Output SFF information as text (default)" &= typFile &= name "T" &= optdef , inputs = def &= args &= typFile } - &= summary "flower v0.6 - Extract information from SFF files" + &= summary "flower v0.6.5 - Extract information from SFF files" &= program "flower" getArgs :: IO Opts