Safe Haskell | Safe-Inferred |
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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 not one, but two different, and indistinguishably so, ways to do it:
- http://www.bcgsc.ca/pipermail/ssrformat/2007-March/000137.html
- http://maq.sourceforge.net/fastq.shtml
- http://en.wikipedia.org/wiki/FASTQ_format
Sanger-style FastQ-format is supported with the (h)read/writeSangerQ functions, and the new IlluminaSolexa-style with (h)readwriteIllumina.
As far as I know, FastQ is only used for nucleotide sequences, never amino acid.
- readFastQ :: FilePath -> IO [Sequence Nuc]
- hReadFastQ :: Handle -> IO [Sequence Nuc]
- parse :: [ByteString] -> Maybe (Either String (Sequence Nuc), [ByteString])
- writeFastQ :: FilePath -> [Sequence Nuc] -> IO ()
- hWriteFastQ :: Handle -> [Sequence Nuc] -> IO ()
- unparse :: Sequence Nuc -> ByteString
- readSangerQ :: FilePath -> IO [Sequence Nuc]
- hReadSangerQ :: Handle -> IO [Sequence Nuc]
- writeSangerQ :: FilePath -> [Sequence Nuc] -> IO ()
- hWriteSangerQ :: Handle -> [Sequence Nuc] -> IO ()
- readIllumina :: FilePath -> IO [Sequence Nuc]
- hReadIllumina :: Handle -> IO [Sequence Nuc]
- writeIllumina :: FilePath -> [Sequence Nuc] -> IO ()
- hWriteIllumina :: Handle -> [Sequence Nuc] -> IO ()
Reading FastQ
readFastQ :: FilePath -> IO [Sequence Nuc]Source
Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead
hReadFastQ :: Handle -> IO [Sequence Nuc]Source
Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead
parse :: [ByteString] -> Maybe (Either String (Sequence Nuc), [ByteString])Source
Writing FastQ
writeFastQ :: FilePath -> [Sequence Nuc] -> IO ()Source
Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead
hWriteFastQ :: Handle -> [Sequence Nuc] -> IO ()Source
Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead
unparse :: Sequence Nuc -> ByteStringSource