[Bioperl-l] warning: Bio::Index::Fastq;

[Ehsan Habibi]

I changed the following part of the code (Bio/Index/Fastq.pm) and now it works perfect :)

# Main indexing loop
while (<$FASTQ>) {
if (/^@[A-Z]/) {







On Tuesday, March 11, 2014 5:40 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
 
On Mar 11, 2014, at 11:16 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:


> On Tue, Mar 11, 2014 at 4:01 PM, EpiMAN <eh_mcb at yahoo.com> wrote:
>> test <http://bioperl.996286.n3.nabble.com/file/n17374/test>
>> 
>> grep -C 10 "^@@DDDDDFFFFFIIIDCBBBB"
> 
> Very helpful - it does look like it came from a valid FASTQ
> (the -- lines are where grep cuts each snippet).
> 
> I think I can explain this, see:
> https://github.com/bioperl/bioperl-live/commit/b45e2d33984cf283b846d7c146ec9e0e9ebae67f
> 
> Chris' hack handled quality lines starting with a single '@'
> sign, but multiple '@' signs like your examples which start
> '@@' instead.
> 
> Peter

We probably need a stricter index method analogous to the Bio::SeqIO::fastq parser.  I’ll see if I can eek out time today to look into it.

chris