[Biojava-dev] sorry about biojava-live/trunk repository mess; was Re: biojava-legacy 1.8.2 release plan

[Hannes Brandstätter-Müller]

Well, it's the 15th now for me, so I'll just delete the
genome.parsers.fastq and consider it frozen from my side.

Hannes

On Wed, Mar 14, 2012 at 21:23, Michael Heuer <heuermh at gmail.com> wrote:
> Hannes Brandstätter-Müller wrote:
>> Andreas Prlic <andreas at sdsc.edu> wrote:
>>
>>> I would tend to split as well. Are you and Hannes in agreement in how
>>> to proceed with this or is there anything we should discuss?  Let me
>>> know if I can help somehow in resolving this.
>>
>> I am in agreement, however I'd like to know if the existing parsers
>> ins the genome.parsers package should be moved to the new location as
>> well or if they should stay.
>
> If you feel that the functionality in sequencing.io.fastq package in
> biojava3-sequencing compares favorably to what is currently in
> genome.parsers.fastq, then I believe we should be fine removing
> genome.parsers.fastq and releasing sequencing.io.fastq in
> biojava3-sequencing for version 3.0.3.
>
> Converting and writing from DNASequence+QualityFeature to FASTQ format
> is not currently supported in sequencing.io.fastq, but adding such (as
> static methods to FastqTools, with additional methods in FastqVariant)
> should not cause binary compatibility issues and could safely be
> released in a 3.0.4 or later release.
>
>
>> I'd prefer to keep anything that parses genomics-related file data
>> somehow together - ideally even genomics and proteomics in their
>> respective subgroups, but I guess since some of the stuff is already
>> present and we should watch compatibility, that train has already left
>> the station.
>>
>> Since I'm new to this as a dev, I'll let you decide where in the
>> package structure we should put the parsers/tools.
>
> Where to put stuff is always difficult to decide, and had I been more
> clever with my svn-foo this might have gone smoother.
>
>   michael