[Bioperl-l] Fastq quality values as strings

Chris Fields cjfields at illinois.edu
Sun Jul 17 21:41:45 UTC 2011

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'.


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
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