[Bioperl-l] fastq parsing problem

[Chris Fields]

On May 12, 2009, at 1:11 PM, Sendu Bala wrote:

> John Marshall wrote:
>> Michael Muratet wrote:
>>> I've got a problem parsing fastq output from the maq aligner. The
>>> parser is throwing an exception for the following record:
>>>
>>> @HWI-EAS146:3:1:2:177#0/1
>>> CTCCGCTNNCTTCTCAG[...]
>>> +
>>> @,AB=>-&&:5).;+*=[...]
>>>
>>> I looked up the line in fastq.pm that does the parsing:
>>>
>>>    116   my ($top,$sequence,$top2,$qualsequence) = [...]
>> This is the fastq parser from 1.5.2 or thereabouts, which had a bug  
>> (the
>> $/ definition just above this code) that prevented it from parsing a
>> record with a quality line starting with "@".  This was probably not
>> recognised as a bug for a long time due to the enduring myth that  
>> fastq
>> quality lines always start with "!".
>
> I see you talked about it in the discussion page, but I think it  
> might be time to change the wiki page as well:
> http://www.bioperl.org/wiki/FASTQ_sequence_format
>
> That caught me out as well. *sigh*

Updated, along with links to the MAQ FASTQ page and Wikipedia.  I'll  
update the module docs as well.

chris