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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
stranger --trgt broken_repeat.vcf --repeats-file variant_catalog_grch38.json
broken_repeat.vcf is attached here: broken_repeat.zip
broken_repeat.vcf
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.
The text was updated successfully, but these errors were encountered:
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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.
The text was updated successfully, but these errors were encountered: