Key errors on `snp_calls()`

malariagen / malariagen-data-python

Analyse MalariaGEN data from Python

https://malariagen.github.io/malariagen-data-python/latest/

MIT License

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Key errors on `snp_calls()` #524

Closed ahernank closed 4 months ago

ahernank commented 4 months ago

Currently the call arrays are built by including keys to GQ,AD,MD data. When these values were empty on the zarr tree, this worked with no issues but after clean-up we get key errors here.

https://github.com/malariagen/malariagen-data-python/blob/ff4907a9b1dc1cebb870c57b1a4f521d5f421239/malariagen_data/anoph/snp_data.py#L900-L908

Screenshot 2024-05-15 at 08 49 37

ahernank commented 4 months ago

Temporarily fixed by using the consolidation inc. GQ,AD,MD data.

Will revisit in the future for a full fix which makes clear the presence/absence of these data.