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sgkit-dev / bio2zarr

Convert bioinformatics file formats to Zarr
Apache License 2.0
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Local alleles updates #286

Closed Will-Tyler closed 4 weeks ago

Will-Tyler commented 4 weeks ago

Overview

From the discussion on #277, we want to change how bio2zarr computes the LAA and LPL fields. In this pull request, bio2zarr localizes only the alleles that are called in the genotype.

This pull request builds on @jeromekelleher's #285.

Testing

I update the existing unit tests to reflect the new expected behavior. I checked the coverage report to confirm that the changes are covered.

coveralls commented 4 weeks ago

Coverage Status

coverage: 98.898% (-0.01%) from 98.91% when pulling 1aaf413cfaced644fd4e95c6b8aee68105c112fb on Will-Tyler:local-alleles-updates into 3d7bfec2f1159a93883337bd9a08e6fef3014369 on sgkit-dev:main.

jeromekelleher commented 4 weeks ago

Thanks @Will-Tyler! Let's merge this and do some testing on real data. I'm interested to see how much actual information we lose here wrt to PL values.