[Open-bio-l] FASTQ support in Biopython, BioPerl, and EMBOSS

[Peter]

On Fri, Jul 31, 2009 at 9:16 AM, Peter Rice<pmr at ebi.ac.uk> wrote:
>
> On the subject or warnings ... While I am happy to issue warnings,
> I suggest we take some care over what happens when someone
> picks the wrong format and a million reads have quality scores out
> of range.
>
> We could, for example, report the first error and then count up so
> we can later (at the end or when another error occurs) say "and
> another 987654 up to ..." and give the latest one.

Yes indeed, a warning for every record which had its quality score
truncated would be madness (given the number of reads you might
have in a FASTQ file). One warning for the whole file would be
enough.

Peter