Bio.Streaming.Bgzf

Buffer builder to assemble Bgzf blocks. The idea is to serialize stuff (BAM and BCF) into a buffer, then bgzf chunks from the buffer. We use a large buffer, and we always make sure there is plenty of space in it (to avoid redundant checks).

Documentation

bgunzip :: MonadIO m => ByteStream m r -> ByteStream m r

Decompresses a bgzip stream. Individual chunks are decompressed in parallel. Leftovers are discarded (some compressed HETFA files appear to have junk at the end).

getBgzfHdr :: Monad m => ByteStream m r -> m (Maybe Int, ByteString, ByteStream m r)

data BB

We manage a large buffer (multiple megabytes), of which we fill an initial portion. We remember the size, the used part, and two marks where we later fill in sizes for the length prefixed BAM or BCF records. We move the buffer down when we yield a piece downstream, and when we run out of space, we simply move to a new buffer. Garbage collection should take care of the rest. Unused mark must be set to (maxBound::Int) so it doesn't interfere with flushing.

Constructors

BB

Fields

• buffer :: !(ForeignPtr Word8)
• size :: !Int
• off :: !Int
• used :: !Int
• mark :: !Int
• mark2 :: !Int

newBuffer :: Int -> IO BB

Creates a buffer.

fillBuffer :: BB -> BgzfTokens -> IO (BB, BgzfTokens)

expandBuffer :: Int -> BB -> IO BB

Creates a new buffer, copying the active content from an old one, with higher capacity. The size of the new buffer is twice the free space in the old buffer, but at least minsz.

encodeBgzf :: MonadIO m => Int -> Stream (Of (Endo BgzfTokens)) m b -> ByteStream m b

Expand a chain of tokens into a buffer, sending finished pieces downstream as soon as possible.

data BgzfTokens

Things we are able to encode. Taking inspiration from binary-serialise-cbor, we define these as a lazy list-like thing and consume it in a interpreter.

Constructors

TkWord32 !Word32 BgzfTokens

TkWord16 !Word16 BgzfTokens

TkWord8 !Word8 BgzfTokens

TkFloat !Float BgzfTokens

TkDouble !Double BgzfTokens

TkString !ByteString BgzfTokens

TkDecimal !Int BgzfTokens

TkMemFill !Int !Word8 BgzfTokens

TkMemCopy !(Vector Word8) BgzfTokens

TkSetMark BgzfTokens

TkEndRecord BgzfTokens

TkEndRecordPart1 BgzfTokens

TkEndRecordPart2 BgzfTokens

TkEnd

TkBclSpecial !BclArgs BgzfTokens

TkLowLevel !Int (BB -> IO BB) BgzfTokens

data BclArgs

Constructors

BclArgs BclSpecialType !(Vector Word8) !Int !Int !Int !Int

data BclSpecialType

Constructors

BclNucsBin

BclNucsAsc

BclNucsAscRev

BclNucsWide

BclQualsBin

BclQualsAsc

BclQualsAscRev

loop_dec_int :: Ptr Word8 -> Int -> IO Int

loop_bcl_special :: Ptr Word8 -> BclArgs -> IO Int

data CompressionError

Constructors

CompressionError !CInt

Instances

Show CompressionError

Defined in Bio.Streaming.Bgzf

Methods

showsPrec :: Int -> CompressionError -> ShowS

show :: CompressionError -> String

showList :: [CompressionError] -> ShowS

Exception CompressionError

Defined in Bio.Streaming.Bgzf

Methods

toException :: CompressionError -> SomeException

fromException :: SomeException -> Maybe CompressionError

displayException :: CompressionError -> String

data DecompressionError

Constructors

DecompressionError !CInt

Instances

Show DecompressionError

Defined in Bio.Streaming.Bgzf

Methods

showsPrec :: Int -> DecompressionError -> ShowS

show :: DecompressionError -> String

showList :: [DecompressionError] -> ShowS

Exception DecompressionError

Defined in Bio.Streaming.Bgzf

Methods

toException :: DecompressionError -> SomeException

fromException :: SomeException -> Maybe DecompressionError

displayException :: DecompressionError -> String