biohazard-1.0.2: bioinformatics support library

Safe HaskellNone



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).



data BB Source #

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.




Show BB Source # 
Instance details

Defined in Bio.Iteratee.Builder


showsPrec :: Int -> BB -> ShowS #

show :: BB -> String #

showList :: [BB] -> ShowS #

newBuffer :: Int -> IO BB Source #

Creates a buffer.

expandBuffer :: Int -> BB -> IO BB Source #

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

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

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

data BgzfTokens Source #

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.

Nullable (Endo BgzfTokens) Source # 
Instance details

Defined in Bio.Iteratee.Builder