Release v0.3.0 #52
Release v0.3.0 #52
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- Includes doctest in tests.
Makes better use of the existing flow in [Automa.jl](https://github.com/BioJulia/Automa.jl/blob/b6997f7415992a82e8538ca6ba8f5f3b5fc9a297/src/Stream.jl#L124-L127).
Improve documentation of flag function
Ok, so this isn't atomic, but we can't upgrade these separately.
BioSequences v3 changed LongDNASeq to LongDNA{N}. We can't assume that
there aren't ambiguous nucleotides in a SAM file, so use the larger
LongDNA variant. The method signatures are also simplified, so simplify
their calls, accordingly.
Same principles apply as updating SAM.sequence
BioSymbols v3 requires Julia 1.6+, so update the "julia" compat entry and remove unit testing against Julia 1.0.
Upgrade BioAlignments to v2.2 & BioSequences to v3
# Conflicts: # Project.toml # test/runtests.jl
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We may update the workflows to match the latest practices - the new write permission is surprising to me. Still, given the origin of the suggestion, I assume it is a security-conscious suggestion.
I'm using this code in production, so I'm otherwise fine with the release. It is, however, clear that the behaviour of the accessor methods needs consolidation in a later release. I'll start a discussion for that.
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
Agreed. My first priority is to get a XAM release out that is compatible with BioAlignments v3, and then work on the API. |
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@CiaranOMara, apparently committing your suggestions removed the "reviewed" status. 😖 Could I get your sign-off again? |
The
developbranch has been accumulating a lot of changes. Let's get them merged and released.