Safe Haskell	None
Language	Haskell2010

Bio.Bam.Writer

Description

Printers for BAM and SAM. BAM is properly supported, SAM can be piped to standard output.

Synopsis

class IsBamRec a where
- pushBam :: a -> BgzfTokens -> BgzfTokens
- unpackBamRec :: a -> BamRec
encodeBamWith :: (IsBamRec a, MonadIO m) => Int -> BamMeta -> Stream (Of a) m r -> ByteStream m r
packBam :: BamRec -> IO BamRaw
writeBamFile :: (IsBamRec a, MonadIO m, MonadMask m) => FilePath -> BamMeta -> Stream (Of a) m r -> m r
writeBamHandle :: (IsBamRec a, MonadIO m) => Handle -> BamMeta -> Stream (Of a) m r -> m r
pipeBamOutput :: (IsBamRec a, MonadIO m) => BamMeta -> Stream (Of a) m r -> m r
pipeSamOutput :: (IsBamRec a, MonadIO m) => BamMeta -> Stream (Of a) m r -> m r

Documentation

class IsBamRec a where Source #

Methods

pushBam :: a -> BgzfTokens -> BgzfTokens Source #

unpackBamRec :: a -> BamRec Source #

Instances

IsBamRec BamRaw Source #
Instance details Defined in Bio.Bam.Writer Methods pushBam :: BamRaw -> BgzfTokens -> BgzfTokens Source # unpackBamRec :: BamRaw -> BamRec Source #
IsBamRec BamRec Source #
Instance details Defined in Bio.Bam.Writer Methods pushBam :: BamRec -> BgzfTokens -> BgzfTokens Source # unpackBamRec :: BamRec -> BamRec Source #
(IsBamRec a, IsBamRec b) => IsBamRec (Either a b) Source #
Instance details Defined in Bio.Bam.Writer Methods pushBam :: Either a b -> BgzfTokens -> BgzfTokens Source # unpackBamRec :: Either a b -> BamRec Source #

encodeBamWith :: (IsBamRec a, MonadIO m) => Int -> BamMeta -> Stream (Of a) m r -> ByteStream m r Source #

Encodes BAM records straight into a dynamic buffer, then BGZF's it. Should be fairly direct and perform well.

packBam :: BamRec -> IO BamRaw Source #

writeBamFile :: (IsBamRec a, MonadIO m, MonadMask m) => FilePath -> BamMeta -> Stream (Of a) m r -> m r Source #

Writes BAM encoded stuff to a file. In reality, it cleverly writes to a temporary file and renames it when done.

writeBamHandle :: (IsBamRec a, MonadIO m) => Handle -> BamMeta -> Stream (Of a) m r -> m r Source #

Writes BAM encoded stuff to a Handle.

pipeBamOutput :: (IsBamRec a, MonadIO m) => BamMeta -> Stream (Of a) m r -> m r Source #

Write BAM encoded stuff to stdout. This sends uncompressed(!) BAM to stdout. Useful for piping to other tools. The output is still wrapped in a BGZF stream, because that's what all tools expect; but the individuals blocks are not compressed.

pipeSamOutput :: (IsBamRec a, MonadIO m) => BamMeta -> Stream (Of a) m r -> m r Source #

write in SAM format to stdout

This is useful for piping to other tools (say, AWK scripts) or for debugging. No convenience functions to send SAM to a file or to compress it exist, because these are stupid ideas.