More refactoring wanted!

[lomereiter]

Hi Marjan,

I would like to merge our libraries for GFF/GTF and SAM/BAM into one. There's also some development of fast FASTA/FASTQ parser going on (see this thread http://forum.dlang.org/thread/[email protected]).

However, code styles are way too different. I've tried to sketch how interfaces should look like (in my opinion) in this gist: https://gist.github.com/lomereiter/5025051 - shouldn't be too hard to make such wrappers on top of existing code.

Waiting for your comments ;)

[mamarjan]

Hey Artem,

Yes, I was thinking the same thing - that we should merge all the libraries into one, say a BioD library :) Until there is something comparable to RubyGems for D, which we could then use for creating something comparable to biogems.

I don't think just making a wrapper would be a good solution, as then we would have to maintain even more code. We should definitely make a goal to merge them, and decide on a common interface style, and maybe even merge all tools into a DBioTools package of some sort...

Some work has also been done in this project: https://gitorious.org/dscience/dscience but I'm not sure what is the current state of this project.

I'm just a bit short on time, but I should be able to take a look during the week.