Bio.HTS.Internal

Documentation

data HTSFile

Opaque data representing the hts file.

withHTSFile :: FilePath -> IOMode -> (Ptr HTSFile -> IO a) -> IO a

htsOpen :: String -> String -> IO (Ptr HTSFile)

Open a hts file.

htsClose :: Ptr HTSFile -> IO ()

Close the hts file.

BGZF

data BGZF

getBgzf :: Ptr HTSFile -> IO (Ptr BGZF)

Get the location of BGZF block.

Bam Header

data BamHdr

Opaque data representing Bam header type.

bamHdrRead :: Ptr BGZF -> IO (Ptr BamHdr)

Get the bam header.

bamHdrWrite :: Ptr BGZF -> Ptr BamHdr -> IO CInt

Save the bam header.

getHeaderText :: Ptr BamHdr -> IO CString

getHeaderSize :: Ptr BamHdr -> IO Int

Bam

data Bam1

bamRead1 :: Ptr BGZF -> Ptr Bam1 -> IO CInt

bamWrite1 :: Ptr BGZF -> Ptr Bam1 -> IO CInt

bamChr :: Ptr BamHdr -> Int -> IO CString

bamEndpos :: Ptr Bam1 -> IO Int

bamIsRev :: Ptr Bam1 -> IO Bool

bamGetSeq :: Ptr Bam1 -> CString -> Int -> IO ()

bamGetQual :: Ptr Bam1 -> CString -> Int -> IO CInt

bamGetCigar :: Ptr Bam1 -> Ptr CInt -> CString -> Int -> IO ()

bamGetAux :: Ptr Bam1 -> IO (Ptr ())

bamGetLAux :: Ptr Bam1 -> IO Int

bamAuxGet :: Ptr Bam1 -> String -> IO (Ptr ())

bamAuxAppend :: Ptr Bam1 -> String -> Char -> Int -> Ptr () -> IO CInt