Closed bicycle1885 closed 4 years ago
I wouldn't use BioAlignments 1.X with BioSequences 2.X, BioAlignments probably won't work with it since the BioSequences API and type hierarchy has changed from 1.X.
A v2.X is being worked towards by Ciaran, who is doing something similar to what I did with BioSequences: removing the extra parsing machinery to their own complete packages and having BioAlignments just be core alignment types and algorithms. When BioAlignments hits 2.0 I'm happy to put it on the BioJuliaRegistry - which I intend to be the place for the 2.X BioJulia ecosystem - especially the new graph-based framework. Older 1.X era stuff can stay on General.
Thank you for your clarification. If there is anything I can help, please feel free to ask me (cc @CiaranOMara).
I believe I have achieved a working separation of the alignment algorithms and the BAM and SAM parsers. @bicycle1885 and @BenJWard it would be grand if you could check the proposed releases:
The https://github.com/BioJulia/BioAlignments.jl/tree/release/v2.0.0 branch would need to be merged into BioAlignments.jl#master and registered before work on XAM.jl v1.0.0 can progress.
Another dependency for the release of XAM v0.1.0 would be GenomicFeatures v2.0.0. (see pre-release/v2.0.0 for an example of what that might look like).
@CiaranOMara v1.0.1 has been released to general. Paving the way for your 2.0 PR.
Hi there!
Today I tried to use BioAlignments.jl along with BioSequences.jl 2.0 and other packages. However, this package is not registered in BioJuliaRegistry and thus it failed to be installed. I've been away for a while so I'm not pretty sure the current release cycle of BioJulia. @BenJWard, could you tell me what I should do here?
BTW, I found BioSequences.jl seems to have the same UUID in both General and BioJuliaRegistry. Is it okay?