UnboundLocalError when decomposing multiallelic variants

[Schmytzi]

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:

• OS: Linux (Red Hat Enterprise Linux 8.10)
• Environment: Running in Apptainer (Container: https://depot.galaxyproject.org/singularity/stranger:0.9.2--pyh7e72e81_0)
• Version: 0.9.2

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

[fellen31]

I believe this might be the same issue?

2025-02-12 17:36:13 compute-0-5.local stranger.cli[41] INFO Running stranger version 0.9.2
2025-02-12 17:36:13 compute-0-5.local stranger.cli[41] INFO Parsing repeats file variant_catalog_grch38.json
2025-02-12 17:36:13 compute-0-5.local stranger.cli[41] INFO Vcf is zipped
Traceback (most recent call last):
  File "/usr/local/bin/stranger", line 10, in <module>
    sys.exit(base_command())
             ^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/click/decorators.py", line 33, in new_func
    return f(get_current_context(), *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/stranger/cli.py", line 189, in cli
    variant_infos = decompose_var(variant_info)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/stranger/utils.py", line 442, in decompose_var
    variant_component_value = individual_value.split(",")[variant_component]
                                                          ^^^^^^^^^^^^^^^^^
UnboundLocalError: cannot access local variable 'variant_component' where it is not associated with a value

Command:

stranger \
    --trgt \
    assuringredbird_repeats.vcf.gz \
    --repeats-file variant_catalog_grch38.json | gzip --no-name > assuringredbird_stranger.vcf.gz

Files:

/home/proj/development/rare-disease/felix/stranger_fix/19d4d2b09070dbca893414da07ce1c/assuringredbird_repeats.vcf.gz
/home/proj/development/rare-disease/felix/stranger_fix/19d4d2b09070dbca893414da07ce1c/assuringredbird_stranger.vcf.gz
/home/proj/development/rare-disease/felix/stranger_fix/19d4d2b09070dbca893414da07ce1c/variant_catalog_grch38.json

[Schmytzi]

Yes, I think that's the one I got.