[Bioperl-l] Fastq quality values as strings

[Chris Fields]

If you are using the latest SeqIO parser, I believe the FASTQ string is returned via next_dataset() only (the raw qual string is passed in to the constructor but is ignored).  This should be pretty fast as no objects are created (the returned data is a hashref), and the qual string key is '-raw_quality'.

chris

On Jul 17, 2011, at 12:33 PM, Nestor Zaburannyi wrote:

> Dear all,
> 
> I want to read quality strings from *.fastq file just as they are, without any conversion to numeric values. Right now, i am reading every 4-th line of the file, but this could break easily. Is there any way to do this within SeqIO parser?
> 
> Sincerely yours
> Nestor
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l