HsHTSLib 1.3.2.2 → 1.3.2.3

raw patch · 2 files changed

+22/−23 lines, 2 filesdep +conduitdep −conduit-combinators

Dependencies added: conduit

Dependencies removed: conduit-combinators

Files

• HsHTSLib.cabal +3/−3
• src/Bio/HTS.hs +19/−20

@@ -1,5 +1,5 @@ name:                HsHTSLib-version:             1.3.2.2+version:             1.3.2.3 synopsis:            High level bindings to htslib. description:         This package provides high level bindings to htslib, a library                      for processing high throughput DNA sequencing data.@@ -7,7 +7,7 @@ license-file:        LICENSE author:              Kai Zhang maintainer:          kai@kzhang.org-copyright:           (c) 2016-2017 Kai Zhang+copyright:           (c) 2016-2018 Kai Zhang category:            Bio build-type:          Simple cabal-version:       >=1.10@@ -28,7 +28,7 @@     , bytestring     , bytestring-lexing     , containers-    , conduit-combinators+    , conduit >=1.3.0     , inline-c >=0.6 && <0.8     , mtl     , template-haskell

@@ -6,7 +6,7 @@  import           Conduit import           Control.Monad-import           Control.Monad.State+import           Control.Monad.Reader import           Data.Bits                (testBit) import qualified Data.ByteString.Char8    as B import           Data.Int@@ -14,6 +14,7 @@ import           Data.Word import           Foreign.C.String import           Foreign.C.Types+import Control.Exception (bracket) import           Foreign.ForeignPtr import           Foreign.Marshal.Array import           Foreign.Ptr@@ -29,32 +30,29 @@  include "htslib/sam.h" -type HeaderState = ResourceT (StateT FileHeader IO)+type HeaderState = ResourceT (ReaderT FileHeader IO) -runBam :: HeaderState a -> IO a-runBam x = evalStateT (runResourceT x) Empty+withBamFile :: FilePath -> (BamFileHandle -> HeaderState a) -> IO a+withBamFile fl action = bracket (openBamFile fl ReadMode) closeBamFile $ \h -> do+    hdr <- readBamHeader h+    runReaderT (runResourceT $ action h) hdr -readBam :: FilePath -> Source HeaderState Bam-readBam fn = bracketP (openBamFile fn ReadMode) closeBamFile $ \h -> do-    hdr <- liftIO (readBamHeader h)-    lift $ put hdr-    source h-  where-    source x = do-        r <- liftIO $ bamRead1 x-        case r of-            Nothing -> return ()-            Just b -> yield b >> source x+readBam :: BamFileHandle -> ConduitT () Bam HeaderState ()+readBam h = do+    r <- liftIO $ bamRead1 h+    case r of+        Nothing -> return ()+        Just b -> yield b >> readBam h {-# INLINE readBam #-} -writeBam :: FilePath -> Sink Bam HeaderState ()+writeBam :: FilePath -> ConduitT Bam o HeaderState () writeBam fn = bracketP (openBamFile fn WriteMode) closeBamFile $ \(BamFileHandle fp) -> do     maybeBam <- await     case maybeBam of         Nothing -> return ()         Just b' -> do             leftover b'-            header <- lift get+            header <- lift ask             case header of                 BamHeader hdr -> do                     err <- liftIO $ [CU.exp| int {@@ -77,12 +75,13 @@         _ -> error ""     return $ BamFileHandle h -closeBamFile :: BamFileHandle -> IO ()-closeBamFile (BamFileHandle h) = [CU.exp| void { hts_close($(htsFile* h)) } |]- readBamHeader :: BamFileHandle -> IO FileHeader readBamHeader (BamFileHandle h) =     BamHeader <$> [CU.exp| bam_hdr_t* { bam_hdr_read($(htsFile* h)->fp.bgzf) } |]++closeBamFile :: BamFileHandle -> IO ()+closeBamFile (BamFileHandle h) = [CU.exp| void { hts_close($(htsFile* h)) } |]+  showBamHeader :: FileHeader -> B.ByteString showBamHeader (BamHeader hdr) = unsafePerformIO $ do