samtools 0.2.3 → 0.2.4

raw patch · 5 files changed

+72/−2 lines, 5 files

Files

• include/samtools.h +3/−0
• samtools.cabal +1/−1
• src/Bio/SamTools/Bam.hs +42/−1
• src/Bio/SamTools/LowLevel.chs +10/−0
• test/SamTest.hs +16/−0

@@ -44,4 +44,7 @@  void bam_init_header_hash(bam_header_t *header); +/* Prototype for bam_aux.c function */+void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);+ #endif /* _samtools_h */

@@ -1,5 +1,5 @@ Name:                samtools-Version:             0.2.3+Version:             0.2.4 Synopsis:            Binding to the C samtools library Description:         Binding to the C samtools library, which reads and                      writes SAM format alignments, both binary and tab-

@@ -1,4 +1,4 @@-{-# LANGUAGE ForeignFunctionInterface #-}+{-# LANGUAGE ForeignFunctionInterface, ScopedTypeVariables #-}  -- | This module provides a fairly direct representation of the -- SAM/BAM alignment format, along with an interface to read and write@@ -30,6 +30,8 @@   , mateTargetID, mateTargetName, mateTargetLen, matePosition, insertSize        , nMismatch, nHits, matchDesc, auxGeti, auxGetf, auxGetd, auxGetA, auxGetZ, auxGet++  , addAuxA, addAuxi, addAuxZ                                                                   , refSpLoc, refSeqLoc                       @@ -292,6 +294,45 @@  instance AuxGet BS.ByteString where   auxGet b str = auxGetZ b str++addAuxA :: Bam1 -> String -> Char -> IO Bam1+addAuxA b0 tag ch+  = alloca $ \(valptr :: (Ptr CChar)) -> do+      poke valptr (CChar . fromIntegral . fromEnum $ ch)+      addAux b0 tag typecchar vallen (castPtr valptr)+  where typecchar = (CChar . fromIntegral . fromEnum $ 'A') +        vallen = fromIntegral $ sizeOf (undefined :: CChar)++addAuxi :: Bam1 -> String -> Int -> IO Bam1+addAuxi b0 tag i+  = alloca $ \(valptr :: (Ptr CInt)) -> do+      poke valptr (CInt . fromIntegral $ i)+      addAux b0 tag typecchar vallen (castPtr valptr)+  where typecchar = (CChar . fromIntegral . fromEnum $ 'i')+        vallen = fromIntegral $ sizeOf (undefined :: CInt)++addAuxZ :: Bam1 -> String -> String -> IO Bam1+addAuxZ b0 tag str+  = withCAString str $ \cstr -> do+      strlen <- lengthArray0 (0 :: CChar) cstr+      addAux b0 tag typecchar (CInt . fromIntegral $ strlen + 1) (castPtr cstr)+  where typecchar = (CChar . fromIntegral . fromEnum $ 'Z')++addAux :: Bam1 -> String -> CChar -> CInt -> Ptr CUChar -> IO Bam1+addAux b0 tag typecchar vallen valptr+  | Prelude.length tag == 2 = withForeignPtr (ptrBam1 b0) $ \pbi0 ->+    do pb' <- bamDup1 pbi0 >>= newForeignPtr bamDestroy1Ptr+       withForeignPtr pb' $ \pbi' ->+         withCAStringLen tag $ \(tagstr, _tagstrlen) ->+           bamAuxAppend pbi' tagstr typecchar vallen valptr+       return $ Bam1 { ptrBam1 = pb', header = header b0 } +  | otherwise = ioError . userError $ "Bad BAM Aux tag " ++ show tag++-- bamAuxAppend :: Bam1Ptr -> Ptr CChar -> CChar -> CInt -> Ptr CUChar -> IO ()++--    else do bptr <- newForeignPtr bamDestroy1Ptr b+--            return . Just $ Bam1 { ptrBam1 = bptr, header = inHeader inh }+  -- | 'Just' the match descriptor alignment field, or 'Nothing' when it -- is absent

@@ -29,6 +29,8 @@                              , bamAuxGet, bamAux2Z, bamAux2i, bamAux2f, bamAux2d, bamAux2A                                                                                                                                , bamInit1, bamDestroy1, bamDestroy1Ptr, bamDup1, bamFormat1++                             , bamAuxAppend                                                            , BamIndexInt, BamIndexPtr                              , bamIndexLoad, bamIndexDestroy@@ -293,6 +295,14 @@  {#fun unsafe bam_format1 as bamFormat1  { id `BamHeaderPtr', id `Bam1Ptr' } -> `CString' id#}++{#fun unsafe bam_aux_append as bamAuxAppend+ { id `Bam1Ptr'+ , id `Ptr CChar'+ , id `CChar'+ , id `CInt'+ , id `Ptr CUChar' }+ -> `()'#}  -- BAM indexing 

@@ -5,6 +5,7 @@ import Control.Exception import Control.Monad import qualified Data.ByteString.Char8 as BS+import Data.List import Data.Maybe import System.Environment import System.Exit@@ -51,6 +52,21 @@                       bracket (Bam.openBamInFile bamin) Bam.closeInHandle $ \hin ->                        Bam.get1 hin >>= maybe (return ()) (parseBam (Bam.inHeader hin))++                     addAuxFields bamin >>= hPutStrLn stderr++addAuxFields :: FilePath -> IO FilePath+addAuxFields inname = let outname = dropExtension inname ++ "-auxa.bam"+                      in bracket (Bam.openBamInFile inname) Bam.closeInHandle $ \hin ->+                        bracket (Bam.openBamOutFile outname (Bam.inHeader hin)) Bam.closeOutHandle $ \hout -> do+                          myloop hin hout 0+                          return outname+  where myloop hin hout idx = Bam.get1 hin >>= maybe (return ()) (\b -> go b >> myloop hin hout (idx + 1))+          where go b = Bam.addAuxA b "XX" 'm' >>= (\b' -> Bam.addAuxi b' "YZ" idx) >>= +                       (\b'' -> Bam.addAuxZ b'' "aa" (digitName $ idx `mod` 10)) >>=+                       Bam.put1 hout+        digitName i | i < 0 || i > 9 = show i+                    | otherwise = ["zero", "one", "two", "three", "four", "five", "six", "seven", "eight", "nine"] !! i  bamToSam :: FilePath -> IO FilePath bamToSam inname = let outname = dropExtension inname ++ "-test.sam"