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

[Peter]

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%. :)

Peter