biohazard 1.1.0 → 1.1.1

raw patch · 5 files changed

+25/−14 lines, 5 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• CHANGELOG.md +4/−0
• biohazard.cabal +1/−1
• src/Bio/Bam/Index.hs +0/−1
• src/Bio/Iteratee/Iteratee.hs +20/−8
• src/Bio/Util/Storable.hs +0/−4

@@ -1,3 +1,7 @@+# 1.1.0 (2018-10-15)++ * Fix for previous workaround.  Repairs writeBamFile.+ # 1.1.0 (2018-10-12)   * Work around changes in exceptions-0.10.0.  This version should

@@ -1,5 +1,5 @@ Name:                biohazard-Version:             1.1.0+Version:             1.1.1 Synopsis:            bioinformatics support library Description:         This is a collection of modules I separated from                      various bioinformatics tools.

@@ -18,7 +18,6 @@ import Bio.Bam.Regions              ( Region(..), Subsequence(..) ) import Bio.Iteratee import Bio.Prelude-import System.Posix.Files           ( fileExist )  import qualified Bio.Bam.Regions                as R import qualified Data.IntMap.Strict             as M

@@ -288,23 +288,35 @@ ioBind_ :: MonadIO m => IO a -> Iteratee s m b -> Iteratee s m b ioBind_ m b = Iteratee $ \onDone onCont -> liftIO m >> runIter b onDone onCont --- | Runs an 'Iteratee' in between an 'IO' action to acquire a resource--- and one to release it.  'Iteratee' can't be an instance of--- 'CIO.MonadMask', so 'CIO.bracket' isn't defined for it.  However, if--- we restrict the acquire/release actions to 'IO', which is the most--- important use case anyway, we can directly implement this weaker--- version.-class MonadIO m => MonadBracketIO m where+class (MonadCatch m, MonadIO m) => MonadBracketIO m where+    altmask :: ((forall a. m a -> m a) -> m b) -> m b++    -- | Runs an 'Iteratee' in between an 'IO' action to acquire a+    -- resource and one to release it.  'Iteratee' can't be an instance+    -- of 'CIO.MonadMask', so 'CIO.bracket' isn't defined for it.+    -- However, if we restrict the acquire/release actions to 'IO',+    -- which is the most important use case anyway, we can directly+    -- implement this weaker version.     bracketIO :: IO a -> (a -> IO b) -> (a -> m c) -> m c  instance MonadBracketIO IO where+    {-# INLINE altmask #-}+    altmask = CIO.mask+     {-# INLINE bracketIO #-}     bracketIO = CIO.bracket  instance (MonadBracketIO m, Nullable s) => MonadBracketIO (Iteratee s m) where+    {-# INLINE altmask #-}+    altmask q = Iteratee $ \od oc -> altmask $ \u -> runIter (q $ ilift u) od oc+     {-# INLINE bracketIO #-}     bracketIO acquire release use =-        Iteratee $ \od oc -> bracketIO acquire release (\h -> runIter (use h) od oc)+      Iteratee $ \od oc -> altmask $ \u ->+          runIter (acquire `ioBind` \resource ->+                   ilift u (use resource) `CIO.onException` liftIO (release resource) >>= \result ->+                   release resource `ioBind_` return result) od oc+  -- | Convert one stream into another with the supplied mapping function. -- This function operates on whole chunks at a time, contrasting to

@@ -19,10 +19,6 @@  import Bio.Prelude -#if defined(HAVE_BYTESWAP_PRIMOPS)-import GHC.Word ( byteSwap16, byteSwap32 )-#endif- peekWord8 :: Ptr a -> IO Word8 peekWord8 = peek . castPtr