├── .cursor └── project.mdc ├── .gitattributes ├── .github └── workflows │ ├── bump.yaml │ ├── merge.yaml │ ├── publish.yaml │ └── test.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CHANGELOG.md ├── Cargo.lock ├── Cargo.toml ├── LICENSE.txt ├── README.md ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── _static │ ├── favicon.ico │ ├── fixed_length.svg │ ├── gvl_logo.png │ ├── gvl_logo.svg │ ├── pad.svg │ ├── personalized_length.svg │ ├── ragged.svg │ ├── shift_trunc.svg │ ├── var_pad.svg │ └── variable_length.svg │ ├── api.md │ ├── basenji2_eval.ipynb │ ├── conf.py │ ├── dataset.md │ ├── faq.md │ ├── geuvadis.ipynb │ ├── index.md │ └── write.md ├── pixi.lock ├── pixi.toml ├── pyproject.toml ├── python └── genvarloader │ ├── __init__.py │ ├── _bigwig.py │ ├── _dataset │ ├── __init__.py │ ├── _genotypes.py │ ├── _impl.py │ ├── _indexing.py │ ├── _intervals.py │ ├── _rag_variants.py │ ├── _reconstruct.py │ ├── _reference.py │ ├── _tracks.py │ ├── _utils.py │ └── _write.py │ ├── _dummy.py │ ├── _fasta.py │ ├── _ragged.py │ ├── _torch.py │ ├── _types.py │ ├── _utils.py │ ├── _variants │ ├── __init__.py │ ├── _records.py │ ├── _sitesonly.py │ └── _utils.py │ ├── data_registry.py │ ├── genvarloader.pyi │ └── py.typed ├── src ├── bigwig.rs └── lib.rs └── tests ├── data ├── bigwig │ ├── generate.py │ ├── sample_0.bw │ └── sample_1.bw ├── generate_ground_truth.py └── source.vcf ├── dataset ├── genotypes │ ├── test_filter_af.py │ ├── test_rag_variants.py │ └── test_reconstruct.py ├── test_dataset.py ├── test_ds_haps.py ├── test_indexing.py ├── test_jitter.py ├── test_realign.py ├── test_subset.py └── test_write.py ├── test_bigwig.rs ├── test_fasta.py ├── test_ref_ds.py ├── test_utils.py ├── tracks ├── bench_cpu_gpu.py ├── test_annot_tracks.py ├── test_i2t_t2i.py ├── test_random_nonoverlapping.py └── utils.py └── variants ├── test_sites.py └── test_variant_utils.py /.cursor/project.mdc: 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