bio-0.3.5: A bioinformatics librarySource codeContentsIndex
Bio.Sequence.FastQ
Contents
Reading FastQ
Writing FastQ
Description

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

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:

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

Synopsis
readFastQ :: FilePath -> IO [Sequence]
hReadFastQ :: Handle -> IO [Sequence]
parse :: [ByteString] -> Maybe (Either String Sequence, [ByteString])
writeFastQ :: FilePath -> [Sequence] -> IO ()
hWriteFastQ :: Handle -> [Sequence] -> IO ()
unparse :: Sequence -> ByteString
Reading FastQ
readFastQ :: FilePath -> IO [Sequence]Source
hReadFastQ :: Handle -> IO [Sequence]Source
parse :: [ByteString] -> Maybe (Either String Sequence, [ByteString])Source
Parse one FastQ entry, suitable for using in unfoldr over lines from a file
Writing FastQ
writeFastQ :: FilePath -> [Sequence] -> IO ()Source
hWriteFastQ :: Handle -> [Sequence] -> IO ()Source
unparse :: Sequence -> ByteStringSource
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