[BioRuby] Fastq performances

[Peter Cock]

On Mon, Mar 28, 2011 at 4:49 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
> Note: output from to_biosequence.output(:fastq_illumina) is not equal to the
> input (still from illumina) the sequence(na and quality is wrapped to 70 chas)
> and the header is repeated. Is it my fault is some part of the code ? I'll put
> the code in github asap.

When writing FASTQ, I would expect BioRuby to omit the repeated header
on the plus line, and NOT to line wrap the sequence and quality lines. This
is deliberate, see http://dx.doi.org/10.1093/nar/gkp1137 for details.

So, if your input did have the repeated header and/or wrapping, then yes,
the input would not match the output.

Peter