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

[Michael Heuer]

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