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Genbank improvements

Open Koeng101 opened this issue 6 months ago • 1 comments

Referencing https://github.com/bebop/poly/issues/434

@carreter is asking for a full rewrite there, but I think I disagree. Useful link to the spec.

  • Feature.GetSequence() always returns a nil error value link This should be fairly easy to fix, it is only referenced once.
  • Gff.AddFeature() code is misleading and mutates Feature state link This doesn't seem like that big of an issue. We can just do a deep copy of the feature and it should be fine.
  • Common Genbank Feature.Type values should be enumerated link This should be pretty easy, just adding strings enums in a few places.

These are all nice improvements, but are all are actually kinda simple to implement. The first will take just a couple lines of changes with zero impact on functionality, the second just takes a copy, and the third is just adding some enums.

I do think a refactor could be in place: In particular, it might be easy to split the parseChecks into functions. I think there is MASSIVE room for improvement in the test suite as well - but honestly, the genbank parser works pretty darn good right now, so I am hesitant to spend the time on the 4th refactor when I could be using my time on better things. Will implement fixes to those 3 things though.

Koeng101 avatar Dec 21 '23 06:12 Koeng101