Bio.Iteratee.Builder

Buffer builder to assemble Bgzf blocks. The plan 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). Whenever a block is ready to be compressed, we stick it into a MVar. When we run out of space, we simply use a new buffer. Multiple threads grab pieces from the MVar, compress them, pass them downstream through another MVar. A final thread restores the order and writes the blocks.

Documentation

data BB

We manage a large buffer (multiple megabytes), of which we fill an initial portion. We remeber 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

Instances

Show BB

newBuffer :: Int -> IO BB

Creates a buffer.

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

expandBuffer :: Int -> BB -> IO BB

Creates a new buffer, copying the content from an old one, with higher capacity.

encodeBgzf :: MonadIO m => Int -> Enumeratee (Endo BgzfTokens) ByteString 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

TkLnString !ByteString BgzfTokens

TkSetMark BgzfTokens

TkEndRecord BgzfTokens

TkEndRecordPart1 BgzfTokens

TkEndRecordPart2 BgzfTokens

TkEnd

TkBclSpecial !BclArgs BgzfTokens

TkLowLevel !Int (BB -> IO BB) BgzfTokens

Instances

Nullable (Endo BgzfTokens)

data BclArgs

Constructors

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

data BclSpecialType

Constructors

BclNucsBin

BclNucsWide

BclNucsAsc

BclNucsAscRev

BclQualsBin

BclQualsAsc

BclQualsAscRev

int_loop :: Ptr Word8 -> Int -> IO Int

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