Bio.Bam.Writer

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

Documentation

class IsBamRec a where

Minimal complete definition

pushBam

Methods

pushBam :: a -> BgzfTokens -> BgzfTokens

Instances

IsBamRec BamRaw

Methods

pushBam :: BamRaw -> BgzfTokens -> BgzfTokens

IsBamRec BamRec

Methods

pushBam :: BamRec -> BgzfTokens -> BgzfTokens

(IsBamRec a, IsBamRec b) => IsBamRec (Either a b)

Methods

pushBam :: Either a b -> BgzfTokens -> BgzfTokens

encodeBamWith :: (MonadIO m, IsBamRec r) => Int -> BamMeta -> Enumeratee [r] ByteString m ()

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

packBam :: BamRec -> IO BamRaw

writeBamFile :: IsBamRec r => FilePath -> BamMeta -> Iteratee [r] IO ()

Writes BAM encoded stuff to a file.

writeBamHandle :: (MonadIO m, IsBamRec r) => Handle -> BamMeta -> Iteratee [r] m ()

Writes BAM encoded stuff to a Handle.

pipeBamOutput :: IsBamRec r => BamMeta -> Iteratee [r] IO ()

write BAM encoded stuff to stdout This send uncompressed BAM to stdout. Useful for piping to other tools.

pipeSamOutput :: MonadIO m => BamMeta -> Iteratee [BamRec] m ()

write in SAM format to stdout This is useful for piping to other tools (say, AWK scripts) or for debugging. No convenience function to send SAM to a file exists, because that's a stupid idea.