Closed nebfield closed 2 months ago
Attention: Patch coverage is 94.44444%
with 1 line
in your changes missing coverage. Please review.
Project coverage is 87.89%. Comparing base (
8fb9c7f
) to head (d9c083e
).
Files | Patch % | Lines |
---|---|---|
...log.match/src/pgscatalog/match/lib/_match/plink.py | 94.44% | 1 Missing :warning: |
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Looking at the coverage reports, the deduplication function hasn't been correctly called since the refactor from the old
pgscatalog-utils
python package (it was accidentally overlooked)Without this patch, duplicated variants IDs are written to scoring files. When newer versions of plink2 use these variants, a warning is emitted:
Duplicate variant IDs used to trigger an error 🤔
For context, this is a problem that happens when combining many scores in parallel which share the same variant ID but have different effect alleles. The correct behaviour should be to split these variants across different scoring files.