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UnboundLocalError when decomposing multiallelic variants #84

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Schmytzi opened this issue Jan 3, 2025 · 0 comments
Open

UnboundLocalError when decomposing multiallelic variants #84

Schmytzi opened this issue Jan 3, 2025 · 0 comments

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@Schmytzi
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Schmytzi commented Jan 3, 2025

Describe the bug
Stranger crashes with an UnboundLocalError when encountering a multiallelic variant where the first sample does not have allele 1.

To Reproduce
Run

stranger --trgt broken_repeat.vcf --repeats-file variant_catalog_grch38.json

broken_repeat.vcf is attached here:
broken_repeat.zip

The variant catalog is the following: https://github.com/Clinical-Genomics/stranger/raw/main/stranger/resources/stranger_repeat_catalog_grch38.json

Expected behavior
Stranger should correctly decompose and annotate the variant (or in this case: emit a warning about the unknown repeat)

System:

Additional context
The crash does not occur if you switch the individuals' genotypes. Then stranger works correctly.

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