[Open-bio-l] White space in FASTQ files?

[Chris Fields]

On Aug 10, 2009, at 8:09 AM, Peter Rice wrote:

> Peter C. wrote:
>> Other than the special case of new lines which we have already  
>> covered
>> (allowed but line wrapping is discouraged), should FASTQ sequence
>> lines (and indeed the quality lines) ever be allowed to include white
>> space (e.g. spaces and tabs)? I've never seen this in a real FASTQ
>> file, and would like to suggest this be considered an error.
>>
>> Comments? Counter suggestions?
>
> I am happy adding a warning message in EMBOSS for this.
>
> If we add too many warning messages then we could break our plan to
> issue one message and follow with "and another 999999 up to ..." if we
> find ourselves issuing more than one warning per sequence.
>
> regards,
>
> Peter Rice

This is quite similar to the 'qual range out-of-bounds for this FASTQ  
variant' warning we discussed earlier.  We could essentially merge  
these to be one and the same.

chris