samtools-conduit 0.1.0.1 → 0.1.1.0

raw patch · 2 files changed

+57/−2 lines, 2 filesdep ~basenew-component:exe:samtools-conduit-copy

Dependency ranges changed: base

Files

• samtools-conduit.cabal +13/−2
• test/SamtoolsConduitCopy.hs +44/−0

@@ -2,7 +2,7 @@ -- documentation, see http://haskell.org/cabal/users-guide/  name:                samtools-conduit-version:             0.1.0.1+version:             0.1.1.0 synopsis:            Conduit interface to SAM/BAM format files through samtools description:         Conduit interface to SAM/BAM format files through samtools homepage:            http://www.ingolia-lab.org/samtools-tutorial.html@@ -18,6 +18,17 @@ library   exposed-modules:     Bio.SamTools.Conduit   -- other-modules:       -  build-depends:       base >= 4.6 && <5, bytestring >= 0.9, samtools >= 0.2.4.1, filepath,+  build-depends:       base ==4.6.*, bytestring >= 0.9, samtools >= 0.2.4.1, filepath,                        transformers, resourcet, conduit >= 1.1   hs-source-dirs:      src++flag Examples+  Description: Build example executables+  Default:     False++executable samtools-conduit-copy+  main-is:             SamtoolsConduitCopy.hs+  other-modules:       Bio.SamTools.Conduit+  build-depends:       base ==4.6.*, bytestring >= 0.9, samtools >= 0.2.4.1, filepath,+                       transformers, resourcet, conduit >= 1.1+  hs-source-dirs:      src, test  

@@ -0,0 +1,44 @@+{-# LANGUAGE ScopedTypeVariables, OverloadedStrings #-}+module Main+       where++import Control.Monad.IO.Class+import Control.Monad.Trans.Resource+import qualified Data.ByteString.Char8 as BS+import qualified Data.Conduit as C+import qualified Data.Conduit.List as C+import Data.Maybe+import Numeric+import System.Environment+import System.FilePath+import System.IO++import qualified Bio.SamTools.Bam as Bam+import qualified Bio.SamTools.Conduit as Bam++main :: IO ()+main = getArgs >>= runWithArgs+  where runWithArgs [ inname ] = copy inname+        runWithArgs _ = do hPutStrLn stderr $ "Specify exactly one input BAM file"++copy :: FilePath -> IO ()+copy infile = do Bam.withBamInFile infile $ \hin ->+                   Bam.withBamOutFile (outfile "-1") (Bam.inHeader hin) $ \hout ->+                   runResourceT $ Bam.sourceHandle hin C.$$ Bam.sinkHandle hout+                 runResourceT $ Bam.sourceBamInFile infile C.$= process C.$$ Bam.sinkBamOutFile (outfile "-2")+                 runResourceT $ Bam.sourceBamInFile infile C.$= enumerate C.$$ Bam.sinkBamOutFile (outfile "-3")+  where outfile suffix = (takeBaseName infile) ++ suffix ++ (takeExtension infile)+                 +process :: (MonadIO m) => C.Conduit Bam.Bam1 m Bam.Bam1+process = C.mapM procOne+  where procOne b0 = let qyseq = fromMaybe "" . Bam.querySeq $ b0+                         nt = BS.foldl' (\n ch -> if ch == 'T' then n+1 else n) 0 qyseq+                         nn = BS.length qyseq+                         fstr = showFFloat (Just 3) ((fromIntegral nt / fromIntegral nn) :: Double) ""+                     in liftIO (Bam.addAuxZ b0 "XX" fstr)++enumerate :: (MonadIO m) => C.Conduit Bam.Bam1 m Bam.Bam1+enumerate = C.mapAccumM procOne 0 >> return ()+  where procOne b0 i = do b' <- liftIO $! Bam.addAuxi b0 "XY" i+                          return (i + 1, b')+