Add basic Zarr parsing support for MaximumParsimonyAncestralAnnotation #14
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percyfal
commented
Dec 1, 2025
percyfal
commented
- Add minimal ZarrVariant class mimicking VCF.Variant
- Add ZarrStore class that returns a ZarrVariant iterator
- Add basic test
- Add minimal ZarrVariant class mimicking VCF.Variant - Add ZarrStore class that returns a ZarrVariant iterator - Add basic test
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Hi @Sendrowski, I have drafted some basic Zarr parsing support. Sorry if you already have gotten started; if not, hopefully we can build on this first draft. I updated the VCFHandler to also deal with Zarr input, keeping the current naming of parameters even though it is inconsistent. Also, I have not added code to actually do any writing but that is easy to fix. Moving forward, I guess you would want to make Zarr support available for all functions, such as DFE estimation and more. I have not looked into that part of the code base, but once a handler is in place this should be pretty straightforward? Best, Per |
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Oh, I should add that you should probably create a new branch for this feature as I created the new branch from master. Also, you may have to add the latest source version of vcztools; I refrained from adding package versions to pyproject for now. |
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Hi Per, Many thanks for the first draft to support Zarr. I created a new branch zarr_support, where I created an abstraction layer for variant file handling. All that remains to be implemented now are Best, |
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Hi, thanks for the quick turnaround! I can certainly help out with Zarr support. With the current abstraction layers I should only have to modify the Zarr classes, right? I think it makes sense as you say to let vcztools / zarr be optional dependencies. Best, Per |
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Hi, Sounds good! Yes, only the Zarr classes should need changes unless I overlooked something. You might also want to create a Best, |
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