Bio.Sequence.FastQ

Support the FastQ format that combines sequence and quality. See:

• http://www.bioperl.org/wiki/FASTQ_sequence_format

Of course, this is yet another vaguely defined pseudo-standard with conflicting definitions. Of course Solexa had to go and invent a different, but indistinguishably so, way to do it:

• http://www.bcgsc.ca/pipermail/ssrformat/2007-March/000137.html
• http://maq.sourceforge.net/fastq.shtml

Currently, we only support the non-Solexa FastQ, adding/subtracting 33 for the quality values.

As far as I know, FastQ is only used for nucleotide sequences, never amino acid.

Reading FastQ

readFastQ :: FilePath -> IO [Sequence Nuc]

hReadFastQ :: Handle -> IO [Sequence Nuc]

parse :: [ByteString] -> Maybe (Either String (Sequence Nuc), [ByteString])

Parse one FastQ entry, suitable for using in unfoldr over lines from a file

Writing FastQ

writeFastQ :: FilePath -> [Sequence a] -> IO ()

hWriteFastQ :: Handle -> [Sequence a] -> IO ()

unparse :: Sequence a -> ByteString