[Bioperl-l] fastq parsing problem

[Sendu Bala]

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*