biohazard-0.6.15: bioinformatics support library

Safe HaskellNone
LanguageHaskell2010

Bio.Iteratee.Builder

Description

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.

Synopsis

Documentation

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.

Constructors

BB 

Fields

Instances

Show BB Source # 

Methods

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.