[Biojava-l] Is a modification of the FASTA parser for my needs easy or should I implement something else?

[Peter Troshin]

There is a nice FastQ parser and many other goodies available from the
http://picard.sourceforge.net/command-line-overview.shtml (just download
the source code) if you need one. 

Regards, 
Peter

>>> Andreas Prlic  12/21/11 3:12 PM >>>
The fastq parser is in the legacy biojava 1.8 and can still be
downloaded if you want. Not sure how hard it would be to migrate it to
biojava3.

A


On Wed, Dec 21, 2011 at 6:44 AM, Hannes Brandstätter-Müller
 wrote:
> On Wed, Dec 21, 2011 at 15:21, Andreas Prlic  wrote:
>> Hi Hannes,
>>
>> if this is a more frequently used file format, would be great to get
a
>> parser for this... Any patches are welcome ! ;-)
>>
>> Andreas
>
> I just put together some kludgy thing that works for me now, but there
> needs to be something done for this.
> I mailed a bit back and forth with Peter, and he pointed me to
> http://news.open-bio.org/news/2009/12/nar-fastq-format/ where Biojava
> is mentioned to understand that quality information too. I guess that
> got lost in the move to 3.0?
>
> If nothing happens until March/April, I'll pick up this as my pet
> project and work to help biojava to support FASTQ and the FASTA/QUAL
> format. But until then I'm totally swamped. If someone else (perhaps
> the one who wrote the FASTA Parser initially) could pick that up, that
> would be great.
>
> Hannes

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