[Biojava-dev] [Biojava-l] FASTA Header Parser

[Michael Heuer]

Hannes Brandstätter-Müller wrote:
> On Wed, Jan 11, 2012 at 22:34, Michael Heuer <heuermh at gmail.com> wrote:
>> Hannes Brandstätter-Müller wrote:
>>> On Wed, Jan 11, 2012 at 16:24, Scooter Willis <HWillis at scripps.edu> wrote:
>>>> Is this a custom header or something output from a sequencing
>>>> instrument/software?
>>>
>>> It's the output of the Roche/454 Titanium FLX Sequencer
>>
>> If you would rather, biojava has support for the FASTQ file format,
>
> we already had this discussion this or last month. FASTQ support is
> still not in 3.0, only in 1.8. I will work on porting that to 3.0 and
> supporting FASTA/QUAL too, most likely, but I will have time for that
> starting in April, after this project that I'm working on currently is
> finished.

There is no reason to port, the fastq package in biojava-legacy is
completely self-contained.  If having it in a separate jar is really a
problem, I could copy it over to the trunk for the next release of
biojava3.

   michael