Bio.Bam.Writer

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

Documentation

class IsBamRec a where

Methods

pushBam :: a -> BgzfTokens -> BgzfTokens

unpackBamRec :: a -> BamRec

Instances

IsBamRec BamRaw

Defined in Bio.Bam.Writer

Methods

pushBam :: BamRaw -> BgzfTokens -> BgzfTokens

unpackBamRec :: BamRaw -> BamRec

IsBamRec BamRec

Defined in Bio.Bam.Writer

Methods

pushBam :: BamRec -> BgzfTokens -> BgzfTokens

unpackBamRec :: BamRec -> BamRec

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

Defined in Bio.Bam.Writer

Methods

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

unpackBamRec :: Either a b -> BamRec

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

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

packBam :: BamRec -> IO BamRaw

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

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

Writes BAM encoded stuff to a Handle.

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

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

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.