Bio.HTS

Documentation

type HeaderState = ResourceT (StateT FileHeader IO)

runBam :: HeaderState a -> IO a

readBam :: FilePath -> Source HeaderState Bam

writeBam :: FilePath -> Sink Bam HeaderState ()

inline_c_ffi_1627476712 :: Ptr HTSFile -> Ptr BamHdr -> IO CInt

inline_c_ffi_1627476697 :: Ptr HTSFile -> Ptr Bam' -> IO CInt

openBamFile :: FilePath -> IOMode -> IO BamFileHandle

inline_c_ffi_1627476753 :: Ptr CChar -> IO (Ptr HTSFile)

inline_c_ffi_1627476761 :: Ptr CChar -> IO (Ptr HTSFile)

closeBamFile :: BamFileHandle -> IO ()

inline_c_ffi_1627476771 :: Ptr HTSFile -> IO ()

readBamHeader :: BamFileHandle -> IO FileHeader

inline_c_ffi_1627476780 :: Ptr HTSFile -> IO (Ptr BamHdr)

showBamHeader :: FileHeader -> ByteString

inline_c_ffi_1627476802 :: Ptr BamHdr -> IO (Ptr CChar)

data SortOrder

Constructors

Unknown

Unsorted

Queryname

Coordinate

getSortOrder :: FileHeader -> SortOrder

bamRead1 :: BamFileHandle -> IO (Maybe Bam)

inline_c_ffi_1627476962 :: Ptr CInt -> Ptr HTSFile -> IO (Ptr Bam')

bamDestory :: FunPtr (Ptr Bam' -> IO ())

getChrId :: Bam -> Int32

Return the chromosome id.

inline_c_ffi_1627476974 :: Ptr Bam' -> IO Int32

getChr :: Ptr BamHdr -> Bam -> Maybe ByteString

Return the chromosome name given the bam file header.

inline_c_ffi_1627476987 :: Ptr BamHdr -> Int32 -> IO (Ptr CChar)

position :: Bam -> Int32

Return the 0-based starting location.

inline_c_ffi_1627476997 :: Ptr Bam' -> IO Int32

endPos :: Bam -> Int32

For a mapped read, this is just position + cigar2rlen. For an unmapped read (either according to its flags or if it has no cigar string), we return position + 1 by convention.

inline_c_ffi_1627477007 :: Ptr Bam' -> IO Int32

queryLen :: Bam -> Int32

Return the query length (read length).

inline_c_ffi_1627477017 :: Ptr Bam' -> IO Int32

isRev :: Bam -> Bool

Whether the query is on the reverse strand.

inline_c_ffi_1627477027 :: Ptr Bam' -> IO CInt

flag :: Bam -> Word16

Return the flag.

inline_c_ffi_1627477038 :: Ptr Bam' -> IO Word16

mapq :: Bam -> Word8

MAPping Quality. It equals −10 log10 Pr{mapping position is wrong}, rounded to the nearest integer. A value 255 indicates that the mapping quality is not available.

inline_c_ffi_1627477048 :: Ptr Bam' -> IO Word8

getSeq :: Bam -> Maybe ByteString

Return the DNA sequence.

inline_c_ffi_1627477058 :: Ptr Bam' -> IO Int32

inline_c_ffi_1627477072 :: Ptr Bam' -> Int32 -> Ptr CChar -> IO ()

qName :: Bam -> ByteString

Get the name of the query.

inline_c_ffi_1627477082 :: Ptr Bam' -> IO (Ptr CChar)

quality :: Bam -> Maybe ByteString

inline_c_ffi_1627477092 :: Ptr Bam' -> IO Int32

inline_c_ffi_1627477101 :: Ptr Bam' -> IO Int8

inline_c_ffi_1627477115 :: Ptr Bam' -> Int32 -> Ptr CChar -> IO ()

cigar :: Bam -> Maybe [(Int, Char)]

inline_c_ffi_1627477125 :: Ptr Bam' -> IO Word16

inline_c_ffi_1627477142 :: Ptr Bam' -> Word16 -> Ptr CInt -> Ptr CChar -> IO ()

mateChrId :: Bam -> Int32

inline_c_ffi_1627477154 :: Ptr Bam' -> IO Int32

mateChr :: Ptr BamHdr -> Bam -> Maybe ByteString

inline_c_ffi_1627477167 :: Ptr BamHdr -> Int32 -> IO (Ptr CChar)

matePos :: Bam -> Int32

0-based

inline_c_ffi_1627477177 :: Ptr Bam' -> IO Int32

tLen :: Bam -> Int32

inline_c_ffi_1627477187 :: Ptr Bam' -> IO Int32

bamToSam :: Ptr BamHdr -> Bam -> Sam

Convert Bam record to Sam record.