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UnboundLocalError when decomposing multiallelic variants #84
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I believe this might be the same issue?
Command:
Files:
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Yes, I think that's the one I got. |
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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
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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