samtools-iteratee 0.1 → 0.1.1

raw patch · 2 files changed

+7/−6 lines, 2 filesdep ~samtools

Dependency ranges changed: samtools

Files

• samtools-iteratee.cabal +4/−4
• src/Bio/SamTools/Iteratee.hs +3/−2

@@ -1,5 +1,5 @@ Name:                samtools-iteratee-Version:             0.1+Version:             0.1.1 Synopsis:            Iteratee interface to SamTools library Description:         Iteratee interface to SamTools library License:             MIT@@ -17,7 +17,7 @@  Library   Exposed-modules:     Bio.SamTools.Iteratee-  Build-depends:       base >= 4.3 && < 5, bytestring >= 0.9 && < 0.10, haskell98, samtools, +  Build-depends:       base >= 4.3 && < 5, bytestring >= 0.9 && < 0.10, haskell98, samtools >= 0.1.1,                         transformers, iteratee >= 0.8 && < 0.9   Hs-Source-Dirs:      src @@ -26,7 +26,7 @@     Buildable: False   Main-Is:             BamFilter.hs   Other-Modules:       Bio.SamTools.Iteratee-  Build-depends:       base >= 4.3 && < 5, bytestring >= 0.9 && < 0.10, haskell98, samtools, +  Build-depends:       base >= 4.3 && < 5, bytestring >= 0.9 && < 0.10, haskell98, samtools >= 0.1.1,                         transformers, iteratee >= 0.8 && < 0.9, monads-tf   Hs-Source-Dirs:      src   Ghc-options:         -Wall@@ -36,7 +36,7 @@     Buildable: False   Main-Is:             BamCount.hs   Other-Modules:       Bio.SamTools.Iteratee-  Build-depends:       base >= 4.3 && < 5, bytestring >= 0.9 && < 0.10, haskell98, samtools, +  Build-depends:       base >= 4.3 && < 5, bytestring >= 0.9 && < 0.10, haskell98, samtools >= 0.1.1,                         transformers, iteratee >= 0.8 && < 0.9, monads-tf, vector   Hs-Source-Dirs:      src   Ghc-options:         -Wall

@@ -9,6 +9,7 @@ import Control.Exception import Control.Monad.IO.Class import qualified Data.ByteString.Char8 as BS+import Data.Int (Int64)  import qualified Bio.SamTools.Bam as Bam import qualified Bio.SamTools.BamIndex as BamIndex@@ -43,12 +44,12 @@                   where onCont k Nothing = step . k $ Iter.Chunk [b]                         onCont k e       = return $ Iter.icont k e -enumIndexRegion :: BamIndex.IdxHandle -> Int -> (Int, Int) -> Iter.Enumerator [Bam.Bam1] IO a+enumIndexRegion :: BamIndex.IdxHandle -> Int -> (Int64, Int64) -> Iter.Enumerator [Bam.Bam1] IO a enumIndexRegion h tid bnds i0 = do   q <- liftIO $ BamIndex.query h tid bnds   enumQuery q i0   -enumBamRegion :: FilePath -> BS.ByteString -> (Int, Int) -> Iter.Enumerator [Bam.Bam1] IO a+enumBamRegion :: FilePath -> BS.ByteString -> (Int64, Int64) -> Iter.Enumerator [Bam.Bam1] IO a enumBamRegion inname seqname bnds i0 = bracket (BamIndex.open inname) BamIndex.close $ \h -> do   tid <- lookupTid . BamIndex.idxHeader $ h   enumIndexRegion h tid bnds i0