chore: merge 0.2.0 feature branch#69
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jsstevenson merged 6 commits intomainfrom Oct 29, 2025
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* Add get_assembly_from_refget_id(), which takes a "SQ.ABCDEFG"-type string and checks against a static mapping of known sequence IDs and their corresponding reference assemblies. In our other use cases, we use SeqRepo for this, but it seems silly to do so when there's a pretty small number of possible associations and they rarely (never?) change. This will enable applications like AnyVar to unit-test liftover protocols without needing to mock or stage a seqrepo interface. * Tighten requirements on input. I think it's more complicated than it's worth to be flexible about whether something is a string or an enum. Previously we might've left this in to be compatible with pyliftover but I think we can afford to be stricter. * update various docs/docstring type things This breaks some interface elements. I'm merging it into a 0.2.0 branch because I think there are one or two other small changes I'd like to make before assessing the impact of a release on places like coolseqtool.
Quality-of-life upgrade. Allows for named access.
Lift over an interval rather than a single set of coordinates. This guards against a bunch of downstream problems, like whether the space in between the start and end can also cleanly lift over, and also saves us a lookup.
I just realized that you need to also know the chromosome name for your refget accession ID to do liftover, so I just moved stuff around in that module so both assembly and chromosome are returned.
korikuzma
approved these changes
Oct 29, 2025
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