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MT workflow not compatible with genmod scoring  #370

@jemten

Description

@jemten

Description of the bug

Email from @fa2k suggests that the MT workflow currently isn't compatible with genmod scoring. Resulting in this error.

[2023-06-23 12:54:34,507] DEBUG   : genmod.commands.score_variants: Adding category score 0 to rank_score
[2023-06-23 12:54:34,507] DEBUG   : genmod.commands.score_variants: Updating rank score to 4
[2023-06-23 12:54:34,507] DEBUG   : genmod.score_variants.score_variant: Checking scores for category splicing
[2023-06-23 12:54:34,507] DEBUG   : genmod.score_variants.score_variant: Checking scores for plugin maxentscan_naitive_alt
Traceback (most recent call last):
  File "/usr/local/bin/genmod", line 10, in <module>
    sys.exit(cli())
  File "/usr/local/lib/python3.9/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.9/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.9/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/click/decorators.py", line 17, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/genmod/commands/score_variants.py", line 173, in score
    category_score = get_category_score(
  File "/usr/local/lib/python3.9/site-packages/genmod/score_variants/score_variant.py", line 55, in get_category_score
    category_scores.append(get_plugin_score(
  File "/usr/local/lib/python3.9/site-packages/genmod/score_variants/score_variant.py", line 27, in get_plugin_score
    value = plugin.get_value(variant_dict=variant, csq_format=csq_format)
  File "/usr/local/lib/python3.9/site-packages/extract_vcf/plugin.py", line 349, in get_value
    for value in self.get_entry(
  File "/usr/local/lib/python3.9/site-packages/extract_vcf/plugin.py", line 136, in get_entry
    entry += split_strings(csq_entry.split('|')[csq_column], self.separators)
IndexError: list index out of range

Workaround for now is to disable the MT workflow if you want scoring on the MT.

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