| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.Bam.Writer
- class IsBamRec a where
- encodeBamWith :: (MonadIO m, IsBamRec r) => Int -> BamMeta -> Enumeratee [r] ByteString m a
- writeBamFile :: IsBamRec r => FilePath -> BamMeta -> Iteratee [r] IO ()
- writeBamHandle :: (MonadIO m, IsBamRec r) => Handle -> BamMeta -> Iteratee [r] m ()
- pipeBamOutput :: IsBamRec r => BamMeta -> Iteratee [r] IO ()
- pipeSamOutput :: MonadIO m => BamMeta -> Iteratee [BamRec] m ()
Documentation
encodeBamWith :: (MonadIO m, IsBamRec r) => Int -> BamMeta -> Enumeratee [r] ByteString m a Source
Encodes BAM records straight into a dynamic buffer, the BGZF's it. Should be fairly direct and perform well.
writeBamFile :: IsBamRec r => FilePath -> BamMeta -> Iteratee [r] IO () Source
writes BAM encoded stuff to a file
XXX This should(!) write indexes on the side---a simple block index
for MapReduce style slicing, a standard BAM index or a name index
would be possible. When writing to a file, this makes even more
sense than when writing to a Handle.
writeBamHandle :: (MonadIO m, IsBamRec r) => Handle -> BamMeta -> Iteratee [r] m () Source
writes BAM encoded stuff to a Handle
We generate BAM with dynamic blocks, then stream them out to the file.
XXX This could write indexes on the side---a simple block index for MapReduce style slicing, a standard BAM index or a name index would be possible.
pipeBamOutput :: IsBamRec r => BamMeta -> Iteratee [r] IO () Source
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 () Source
Printers for BAM. We employ an Iteratee interface, and we strive
to keep BAM records in their encoded form. This is most compact and
often faster, since it saves the time for repeated decoding and
encoding, if that's not strictly needed.
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.