samtools-enumerator (empty) → 0.1

raw patch · 4 files changed

+117/−0 lines, 4 filesdep +basedep +bytestringdep +enumeratorsetup-changed

Dependencies added: base, bytestring, enumerator, haskell98, samtools, transformers

Files

• LICENSE +21/−0
• Setup.hs +2/−0
• samtools-enumerator.cabal +18/−0
• src/Bio/SamTools/Enumerator.hs +76/−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 +1,18 @@+Name:                samtools-enumerator+Version:             0.1+Synopsis:            Enumerator interface to SamTools library+Description:         Enumerator interface to SamTools library+License:             MIT+License-file:        LICENSE+Author:              Nicholas Ingolia+Maintainer:          nick@ingolia.org+Category:            Bio++Build-type:          Simple+Cabal-version:       >=1.4++Library+  Exposed-modules:     Bio.SamTools.Enumerator+  Build-depends:       base >= 4.3 && < 5, bytestring, haskell98, transformers, enumerator >= 0.4.7 && < 0.5, samtools >= 0.1.1 && < 0.2+  Hs-Source-Dirs:      src+

@@ -0,0 +1,76 @@+module Bio.SamTools.Enumerator +       (+       -- | BAM/SAM enumeration+         enumInHandle+       , enumTam, enumTamWithIndex, enumBam+       -- | Indexed BAM region enumeration+       , enumQuery, enumIndexRegion, enumBamRegion+       -- | BAM/SAM iteration+       , iterHandle+       )+       where++import Control.Exception (bracket, bracket_, finally)+import Control.Monad+import Control.Monad.IO.Class+import qualified Data.ByteString.Char8 as BS+import Data.Int (Int64)+import Data.List+import Data.Maybe++import qualified Bio.SamTools.Bam as Bam+import qualified Bio.SamTools.BamIndex as BamIndex+import qualified Data.Enumerator as E++-- | Enumerate over the contents of a BAM/SAM alignment input handle+enumInHandle :: (MonadIO m) => Bam.InHandle -> E.Enumerator Bam.Bam1 m a+enumInHandle inh = loop+  where loop (E.Continue k) = (liftIO $ Bam.get1 inh) >>= maybe eof next+          where eof = E.returnI (E.Continue k)+                next b = k (E.Chunks [b]) E.>>== loop+        loop step = E.returnI step++-- | Enumerate over the contents of a TAM (tab-delimited text) alignment file+enumTam :: FilePath -> E.Enumerator Bam.Bam1 IO a+enumTam inname step = E.Iteratee $ liftIO $ bracket (Bam.openTamInFile inname) Bam.closeInHandle $ \h ->+  E.runIteratee $ enumInHandle h step++-- | Enumerate over the contents of a TAM file with a separate target sequence index+enumTamWithIndex :: FilePath -> FilePath -> E.Enumerator Bam.Bam1 IO a+enumTamWithIndex inname idxname step+  = E.Iteratee $ liftIO $ bracket (Bam.openTamInFileWithIndex inname idxname) Bam.closeInHandle $ \h ->+  E.runIteratee $ enumInHandle h step++-- | Enumerate over the contents of a BAM (binary) alignment file+enumBam :: FilePath -> E.Enumerator Bam.Bam1 IO a+enumBam inname step = E.Iteratee $ liftIO $ bracket (Bam.openBamInFile inname) Bam.closeInHandle $ \h ->+  E.runIteratee $ enumInHandle h step++-- | Enumerate over the results of a query into a sorted, indexed BAM file+enumQuery :: BamIndex.Query -> E.Enumerator Bam.Bam1 IO a+enumQuery q = loop+  where loop (E.Continue k) = (liftIO $ BamIndex.next q) >>= maybe end next+            where end = E.returnI (E.Continue k)+                  next b = k (E.Chunks [b]) E.>>== loop+        loop step = E.returnI step+        +-- | Enumerate over the reads in a region from an indexed BAM file input handle+enumIndexRegion :: BamIndex.IdxHandle -> Int -> (Int64, Int64) -> E.Enumerator Bam.Bam1 IO a+enumIndexRegion h tid bnds step = E.Iteratee $ do +  q <- liftIO $ BamIndex.query h tid bnds +  E.runIteratee $ enumQuery q step++-- | Enumerate over the reads in a region from a sorted, indexed BAM file+enumBamRegion :: FilePath -> BS.ByteString -> (Int64, Int64) -> E.Enumerator Bam.Bam1 IO a+enumBamRegion inname seqname bnds step = E.Iteratee $ liftIO $ bracket (BamIndex.open inname) (BamIndex.close) $ \h -> do+  tid <- lookupTid $ BamIndex.idxHeader h+  E.runIteratee $ enumIndexRegion h tid bnds step+    where lookupTid = maybe noTid return . findIndex ((== seqname) . Bam.name) . Bam.targetSeqList+          noTid = ioError . userError $ "Target " ++ show seqname ++ " not found in " ++ show inname+          +iterHandle :: Bam.OutHandle -> E.Iteratee Bam.Bam1 IO ()+iterHandle h = E.continue step+  where step E.EOF = E.yield () E.EOF+        step (E.Chunks []) = E.continue step+        step (E.Chunks bs) = do liftIO $ forM_ bs $ Bam.put1 h+                                E.continue step