support heteroplasmy/homoplasmy

[aslgraefe]

When trying to run GPSEA on a cohort with mitochondrial variants and heteroplasmic/homoplasmic variants we received a ValueError (see below). It would be interesting to have GPSEA support mitochondrial diseases, too.

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[8], [line 5](vscode-notebook-cell:?execution_count=8&line=5)
      [3](vscode-notebook-cell:?execution_count=8&line=3) cohort_creator = configure_caching_cohort_creator(hpo)
      [4](vscode-notebook-cell:?execution_count=8&line=4) pp_dir = '/Users/adam/Documents/test/rarelink/irud_test/mito_pheno/phenopackets'
----> [5](vscode-notebook-cell:?execution_count=8&line=5) cohort, qc_results = load_phenopacket_folder(pp_dir, cohort_creator)

File ~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:440, in load_phenopacket_folder(pp_directory, cohort_creator, validation_policy)
    [437](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:437) pp_files = _find_phenopacket_files(pp_directory)
    [439](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:439) # Map to patients
--> [440](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:440) return load_phenopacket_files(
    [441](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:441)     pp_files=pp_files,
    [442](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:442)     cohort_creator=cohort_creator,
    [443](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:443)     validation_policy=validation_policy,
    [444](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:444) )

File ~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:464, in load_phenopacket_files(pp_files, cohort_creator, validation_policy)
    [447](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:447) def load_phenopacket_files(
    [448](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:448)     pp_files: typing.Iterator[str],
    [449](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:449)     cohort_creator: CohortCreator[Phenopacket],
    [450](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:450)     validation_policy: typing.Literal["permissive", "lenient", "strict"] = "permissive",
    [451](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:451) ) -> typing.Tuple[Cohort, PreprocessingValidationResult]:
    [452](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:452)     """
    [453](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:453)     Load phenopacket JSON files, validate the data, and assemble into a :class:`~gpsea.model.Cohort`.
    [454](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_config.py:454) 
...
     [73](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_phenopacket.py:73)     return Genotype.HEMIZYGOUS
     [74](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_phenopacket.py:74) else:
---> [75](https://file+.vscode-resource.vscode-cdn.net/Users/adam/Documents/git/gpsea-cs/irud_test/~/Documents/git/gpsea-cs/gpcvenv/lib/python3.12/site-packages/gpsea/preprocessing/_phenopacket.py:75)     raise ValueError(f"Unknown genotype {genotype}")

ValueError: Unknown genotype heteroplasmic