├── .copier-answers.yml ├── .github ├── ISSUE_TEMPLATE │ ├── 1-bug.md │ ├── 2-feature.md │ ├── 3-docs.md │ ├── 4-change.md │ └── config.yml └── workflows │ ├── ci.yml │ ├── docs.yml │ └── release.yml ├── .gitignore ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── Makefile ├── README.md ├── benchmark ├── __init__.py ├── annotations2parquet.py ├── cli.py ├── compute_id.py ├── hive.py ├── parse_vcf.py └── struct_bench.py ├── config ├── benchmark.ini ├── black.toml ├── coverage.ini ├── git-changelog.toml ├── mypy.ini ├── pytest.ini └── ruff.toml ├── docs ├── .overrides │ └── partials │ │ ├── comments.html │ │ └── path-item.html ├── benchmark.md ├── changelog.md ├── code_of_conduct.md ├── contributing.md ├── credits.md ├── css │ ├── material.css │ └── mkdocstrings.css ├── index.md ├── javascripts │ └── mathjax.js ├── js │ └── feedback.js ├── license.md ├── logo.svg ├── reference │ └── api.md └── usage.md ├── duties.py ├── mkdocs.yml ├── pyproject.toml ├── scripts ├── gen_benchmark_plot.py ├── gen_credits.py ├── get_version.py ├── make └── make.py ├── src └── variantplaner │ ├── __init__.py │ ├── __main__.py │ ├── cli │ ├── __init__.py │ ├── metadata.py │ ├── parquet2vcf.py │ ├── struct.py │ ├── transmission.py │ └── vcf2parquet.py │ ├── exception.py │ ├── generate.py │ ├── io │ ├── __init__.py │ └── vcf.py │ ├── normalization.py │ ├── objects │ ├── __init__.py │ ├── annotations.py │ ├── contigs_length.py │ ├── csv.py │ ├── genotypes.py │ ├── pedigree.py │ ├── variants.py │ ├── vcf.py │ └── vcf_header.py │ ├── py.typed │ └── struct │ ├── __init__.py │ ├── genotypes.py │ └── variants.py ├── tests ├── __init__.py ├── conftest.py ├── data │ ├── 31C177.ped │ ├── all_info.vcf.gz │ ├── annotations.csv │ ├── grch38.92.csv │ ├── metadata.csv │ ├── metadata.json │ ├── metadata.jsonl │ ├── metadata.parquet │ ├── missing_father.ped │ ├── multi_child.ped │ ├── multi_format.vcf │ ├── no_genotypes.annotations.parquet │ ├── no_genotypes.parquet │ ├── no_genotypes.variants.parquet │ ├── no_genotypes.vcf │ ├── no_genotypes.vcf2parquet2vcf.vcf │ ├── no_info.csv │ ├── no_info.genotypes.parquet │ ├── no_info.parquet │ ├── no_info.parquet2vcf.vcf │ ├── no_info.parquet2vcf_genotypes.vcf │ ├── no_info.tsv │ ├── no_info.variants.parquet │ ├── no_info.vcf │ ├── no_info.vcf2parquet2vcf.vcf │ ├── no_info_no_gt.genotypes.parquet │ ├── no_info_no_gt.vcf │ ├── one.g.parquet │ ├── one_line.ped │ ├── only_genotype_31C177.parquet │ ├── only_header.vcf │ ├── sample.parquet │ ├── sample.ped │ ├── sv.genotypes.parquet │ ├── sv.parquet │ ├── sv.variants.parquet │ ├── sv.vcf │ ├── three.g.parquet │ ├── transmission.parquet │ ├── transmission_multi.parquet │ └── two.g.parquet ├── test_cli.py ├── test_cli_help.py ├── test_exception.py ├── test_generate.py ├── test_io_ped.py ├── test_normalization.py ├── test_struct_genotypes.py ├── test_struct_variants.py ├── test_vcf.py └── test_vcf_header.py └── variantid ├── .gitignore ├── Makefile ├── bench.py ├── 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