├── .gitignore ├── .pre-commit-config.yaml ├── CHANGES.rst ├── LICENSE.txt ├── README.md ├── docs ├── Makefile ├── _static │ ├── alabaster.css_t │ └── custom.css ├── _templates │ ├── about.html │ ├── navigation.html │ └── slim_searchbox.html ├── acmg_guideline.rst ├── changelog.rst ├── cli.rst ├── conf.py ├── contents.rst ├── development.rst ├── index.rst ├── installation.rst ├── internals │ ├── acmg_modules.rst │ ├── classifier.rst │ ├── config.rst │ ├── console.rst │ ├── csq.rst │ ├── custom_modules.rst │ ├── index.rst │ ├── io.rst │ ├── result.rst │ └── variant.rst ├── make.bat └── prepare_inputs.rst ├── mypy.ini ├── poetry.lock ├── pyproject.toml ├── scripts └── debug_example.py ├── setup.cfg ├── src └── charger │ ├── __init__.py │ ├── acmg_modules │ ├── __init__.py │ └── pathogenic.py │ ├── argtype.py │ ├── classifier.py │ ├── config.py │ ├── console.py │ ├── csq.py │ ├── custom_modules │ ├── __init__.py │ └── pathogenic.py │ ├── io.py │ ├── result.py │ └── variant.py ├── tests ├── __init__.py ├── conftest.py ├── examples │ ├── 10.1056_NEJMoa1508054_S4_AD_vep85.sorted.vcf.gz │ ├── 10.1056_NEJMoa1508054_S4_AD_vep85.sorted.vcf.gz.csi │ ├── annotations │ │ ├── clinvar_chrom_22_only.b37.tsv.gz │ │ ├── clinvar_chrom_22_only.b37.tsv.gz.tbi │ │ ├── grch37_pathogenic_variants.vcf.gz │ │ ├── inheritance_gene_table.tsv.gz │ │ └── pp2_gene_list.txt.gz │ ├── grch37_vep85_5_variants.vcf │ ├── grch38_brca2_ashkenazi_jewish_founder.vcf │ ├── grch38_vep95_50_variants.bcf │ ├── grch38_vep95_50_variants.bcf.csi │ ├── grch38_vep95_50_variants.info_fixed.vcf.gz │ ├── grch38_vep95_50_variants.info_fixed.vcf.gz.csi │ ├── grch38_vep95_50_variants.vcf.gz │ └── grch38_vep95_50_variants.vcf.gz.csi ├── test_argtypes.py ├── test_classifier │ ├── test_clinvar_match.py │ ├── test_data_structure.py │ └── test_internal_steps.py ├── test_config.py ├── test_console.py ├── test_files │ └── example.csv.gz ├── test_io.py ├── test_pytest_examples.py └── test_variant.py ├── tox.ini └── 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