biohazard 1.0.2 → 1.0.3

raw patch · 5 files changed

+13/−18 lines, 5 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• biohazard.cabal +1/−1
• src/Bio/Bam/Rec.hs +1/−1
• src/Bio/Iteratee/Bgzf.hsc +1/−3
• src/Bio/Iteratee/IO.hs +5/−4
• src/Bio/Iteratee/Iteratee.hs +5/−9

@@ -1,5 +1,5 @@ Name:                biohazard-Version:             1.0.2+Version:             1.0.3 Synopsis:            bioinformatics support library Description:         This is a collection of modules I separated from                      various bioinformatics tools.

@@ -216,7 +216,7 @@ -- | Smart constructor.  Makes sure we got a at least a full record. {-# INLINE bamRaw #-} bamRaw :: FileOffset -> Bytes -> BamRaw-bamRaw o s = if good then BamRaw o s else error $ "broken BAM record " ++ show (S.length s, m) ++ show m+bamRaw o s = if good then BamRaw o s else error $ "broken BAM record " ++ shows (S.length s, m) " " ++ show (S.unpack (S.take 10 s))   where     good | S.length s < 32 = False          | otherwise       = S.length s >= sum m

@@ -94,9 +94,7 @@             seek $ o `shiftR` 16             eneeCheckIfDonePass (go (o `shiftR` 16) emptyQ) $ do                 block'drop . fromIntegral $ o .&. 0xffff-                k (EOF Nothing)-                -- I think, 'seek' swallows one 'Stream' value on-                -- purpose, so we have to give it a dummy one.+                liftI k      block'drop sz = liftI $ \s -> case s of         EOF _ -> throwErr $ setEOF s

@@ -57,10 +57,11 @@                     else loop . k $ Chunk s      onCont k j@(Just e) = case fromException e of-      Just (SeekException off) -> do-                   liftIO . void $ fdSeek fd AbsoluteSeek (fromIntegral off)-                   loop $ liftI k-      Nothing -> return (icont k j)+        Just (SeekException off) -> do+            liftIO . void $ fdSeek fd AbsoluteSeek (fromIntegral off)+            onCont k Nothing++        Nothing -> return (icont k j)   

@@ -11,7 +11,6 @@   ,throwRecoverableErr   ,checkErr   -- ** Basic Iteratees-  ,unitIter   ,skipToEof   ,isStreamFinished   -- ** Iteratee composition@@ -107,10 +106,6 @@ -- ------------------------------------------------------------------------ -- Parser combinators --- |The identity iteratee.  Doesn't do any processing of input.-unitIter :: (NullPoint s) => Iteratee s m ()-unitIter = idone () (Chunk emptyP)- -- |Get the stream status of an iteratee. isStreamFinished :: (Nullable s) => Iteratee s m (Maybe SomeException) isStreamFinished = liftI check@@ -131,9 +126,10 @@   -- |Seek to a position in the stream-seek :: (NullPoint s) => FileOffset -> Iteratee s m ()-seek o = throwRecoverableErr (toException $ SeekException o) (const unitIter)+seek :: Nullable s => FileOffset -> Iteratee s m ()+seek o = throwRecoverableErr (toException $ SeekException o) (idone ()) + -- | Map a monadic function over the chunks of the stream and ignore the -- result.  Useful for creating efficient monadic iteratee consumers, e.g. --@@ -326,7 +322,7 @@   -> Enumeratee s s' m a convStream fi = eneeCheckIfDonePass check   where-    check k (Just e) = throwRecoverableErr e (const unitIter) >> check k Nothing+    check k (Just e) = throwRecoverableErr e (idone ()) >> check k Nothing     check k _ = isStreamFinished >>= maybe (step k) (idone (liftI k) . EOF . Just)     step k = fi >>= eneeCheckIfDonePass check . k . Chunk {-# INLINABLE convStream #-}@@ -341,7 +337,7 @@   -> Enumeratee s s' m a unfoldConvStream f acc0 = eneeCheckIfDonePass (check acc0)   where-    check acc k (Just e) = throwRecoverableErr e (const unitIter) >> check acc k Nothing+    check acc k (Just e) = throwRecoverableErr e (idone ()) >> check acc k Nothing     check acc k _ = isStreamFinished >>=                     maybe (step acc k) (idone (liftI k) . EOF . Just)     step acc k = f acc >>= \(acc', s') ->