samtools-conduit (empty) → 0.1.0.0

raw patch · 4 files changed

+110/−0 lines, 4 filesdep +basedep +bytestringdep +conduitsetup-changed

Dependencies added: base, bytestring, conduit, filepath, resourcet, samtools, transformers

Files

• LICENSE +21/−0
• Setup.hs +2/−0
• samtools-conduit.cabal +23/−0
• src/Bio/SamTools/Conduit.hs +64/−0

@@ -0,0 +1,21 @@+The MIT License++Copyright (c) 2011 Nicholas Ingolia++Permission is hereby granted, free of charge, to any person obtaining a copy+of this software and associated documentation files (the "Software"), to deal+in the Software without restriction, including without limitation the rights+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell+copies of the Software, and to permit persons to whom the Software is+furnished to do so, subject to the following conditions:++The above copyright notice and this permission notice shall be included in+all copies or substantial portions of the Software.++THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN+THE SOFTWARE.

@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain

@@ -0,0 +1,23 @@+-- Initial samtools-conduit.cabal generated by cabal init.  For further +-- documentation, see http://haskell.org/cabal/users-guide/++name:                samtools-conduit+version:             0.1.0.0+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+license:             MIT+license-file:        LICENSE+author:              Nicholas Ingolia+maintainer:          nick@ingolia.org+-- copyright:           +category:            Bioinformatics+build-type:          Simple+cabal-version:       >=1.8++library+  exposed-modules:     Bio.SamTools.Conduit+  -- other-modules:       +  build-depends:       base ==4.6.*, bytestring >= 0.9, samtools >= 0.2.4.1, filepath,+                       transformers, resourcet, conduit >= 1.1+  hs-source-dirs:      src

@@ -0,0 +1,64 @@+{-# LANGUAGE RankNTypes #-}+module Bio.SamTools.Conduit+       where++import Control.Monad.IO.Class+import Control.Monad.Trans.Resource+import qualified Data.Conduit as C+import qualified Data.Conduit.List as C++import qualified Bio.SamTools.Bam as Bam+import qualified Bio.SamTools.BamIndex as BamIdx++import System.FilePath++-- | Streams the alignments read from a 'Bam.InHandle'+sourceHandle :: (MonadIO m) => Bam.InHandle -> C.Producer m Bam.Bam1+sourceHandle inh = go+  where go = (liftIO $ Bam.get1 inh) >>= maybe (return ()) (\b -> C.yield b >> go)++-- | Streams the alignments read from a BAM format (binary) file+sourceBamInFile :: (MonadResource m) => FilePath -> C.Producer m Bam.Bam1+sourceBamInFile infile = C.bracketP (Bam.openBamInFile infile) Bam.closeInHandle sourceHandle++-- | Streams the alignments read from a TAM format (tab-delimited text) file+sourceTamInFile :: (MonadResource m) => FilePath -> C.Producer m Bam.Bam1+sourceTamInFile infile = C.bracketP (Bam.openTamInFile infile) Bam.closeInHandle sourceHandle++-- | Streams the alignments read from a 'BamIdx.Query' set of query results+sourceQuery :: (MonadIO m) => BamIdx.Query -> C.Producer m Bam.Bam1+sourceQuery qy = go+  where go = (liftIO $ BamIdx.next qy) >>= maybe (return ()) (\b -> C.yield b >> go)++-- | Stream incoming alignments into a 'Bam.OutHandle'+sinkHandle :: (MonadIO m) => Bam.OutHandle -> C.Consumer Bam.Bam1 m ()+sinkHandle outh = C.mapM_ (liftIO . Bam.put1 outh)++-- | Stream incoming alignments into a BAM-format output file with header specified+sinkBamOutFileWithHeader :: (MonadResource m) => FilePath -> Bam.Header -> C.Consumer Bam.Bam1 m ()+sinkBamOutFileWithHeader outfile hdr = C.bracketP (Bam.openBamOutFile outfile hdr) Bam.closeOutHandle sinkHandle++-- | Stream incoming alignments into a BAM-format output file using+-- the target sequence headers from the first 'Bam.Bam1' alignment.+sinkBamOutFile :: (MonadResource m) => FilePath -> C.Consumer Bam.Bam1 m ()+sinkBamOutFile outfile = C.await >>= \mb -> case mb of+                                              Nothing -> return ()+                                              Just b -> C.bracketP (openAndPut b) Bam.closeOutHandle sinkHandle+  where openAndPut b = do outh <- Bam.openBamOutFile outfile (Bam.header b)+                          liftIO . Bam.put1 outh $! b+                          return outh++-- | Stream incoming alignments into a TAM-format output file with header specified+sinkTamOutFileWithHeader :: (MonadResource m) => FilePath -> Bam.Header -> C.Consumer Bam.Bam1 m ()+sinkTamOutFileWithHeader outfile hdr = C.bracketP (Bam.openTamOutFile outfile hdr) Bam.closeOutHandle sinkHandle++-- | Stream incoming alignments into a TAM-format output file using+-- the target sequence headers from the first 'Bam.Bam1' alignment.+sinkTamOutFile :: (MonadResource m) => FilePath -> C.Consumer Bam.Bam1 m ()+sinkTamOutFile outfile = C.await >>= \mb -> case mb of+                                              Nothing -> return ()+                                              Just b -> C.bracketP (openAndPut b) Bam.closeOutHandle sinkHandle+  where openAndPut b = do outh <- Bam.openTamOutFile outfile (Bam.header b)+                          liftIO . Bam.put1 outh $! b+                          return outh+