[Open-bio-l] More FASTQ examples for cross project testing

[Michael Heuer]

On Tue, 1 Sep 2009, Peter wrote:

> On Tue, Sep 1, 2009 at 5:03 PM, Chris Fields<cjfields at illinois.edu> wrote:
> >
> > On Sep 1, 2009, at 10:28 AM, Peter wrote:
> >
> >> All the error_*.fastq files are correctly rejected by BioPerl, except
> >> those with invalid characters in the quality string (e.g. a delete)
> >> which are treated as a warning condition (rather than aborting
> >> with an exception):
> >>
> >> error_qual_del.fastq
> >> error_qual_escape.fastq
> >> error_qual_null.fastq
> >> error_qual_space.fastq
> >> error_qual_tab.fastq
> >> error_qual_unit_sep.fastq
> >> error_qual_vtab.fastq
> >>
> >> Presumably this is in line with (Bio)Perl norms? i.e. Make a best guess
> >> at what the file is trying trying to say, issue a warning, but continue?
> >>
> >> In Biopython (in line with Python norms), we don't try to guess. Giving
> >> an error and aborting is the only clear and unambiguous action.
> >>
> >> Would it suffice to agree that all the OBF projects will read these
> >> error_*.fastq files and either raise an exception (abort), or at least
> >> issue a warning?
> >
> > I would rather throw on those; I can easily change that behavior to do
> > whatever the consensus is.
> >
> > chris
>
> If you (Chris) would prefer BioPerl to throw an exception and abort on
> these error cases, I would support that 100%. :)

I haven't got quite that far yet, this evening perhaps, BioJava will
behave the same.

   michael