├── .binder ├── postBuild ├── requirements.txt └── runtime.txt ├── .devcontainer └── devcontainer.json ├── .github ├── CODEOWNERS └── workflows │ ├── python-cqa.yml │ └── release.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── CLAUDE.md ├── LICENSE ├── Makefile ├── README.md ├── docker-compose.yml ├── docs ├── changelog │ ├── 0.5 │ │ ├── 0.5.0.clog │ │ ├── 0.5.0.rst │ │ └── Makefile │ └── 0.6 │ │ ├── 0.6.0.clog │ │ ├── 0.6.0.rst │ │ ├── 0.6.1.clog │ │ ├── 0.6.1.rst │ │ ├── 0.6.2.clog │ │ ├── 0.6.2.rst │ │ ├── 0.6.3.clog │ │ ├── 0.6.3.rst │ │ ├── 0.6.4.clog │ │ ├── 0.6.4.rst │ │ └── Makefile ├── extras │ └── vcf_annotator.md └── setup_help │ ├── m1_mac_setup.md │ └── uta_installation.md ├── misc └── githooks │ └── post-checkout ├── notebooks └── getting_started │ ├── 1_Quick_Start.ipynb │ ├── 2_Exploring_the_SeqRepo_DataProxy.ipynb │ ├── 3_Basic_Models.ipynb │ ├── 4_Exploring_the_AlleleTranslator.ipynb │ ├── 5_Exploring_the_CnvTranslator.ipynb │ ├── 6_Upcoming_features.ipynb │ └── README.md ├── pyproject.toml ├── src └── ga4gh │ ├── core │ ├── __init__.py │ ├── digests.py │ ├── enderef.py │ ├── identifiers.py │ ├── models.py │ └── pydantic.py │ └── vrs │ ├── __init__.py │ ├── dataproxy.py │ ├── enderef.py │ ├── extras │ ├── __init__.py │ ├── annotator │ │ ├── __init__.py │ │ ├── cli.py │ │ └── vcf.py │ ├── decorators.py │ ├── object_store.py │ └── translator.py │ ├── models.py │ ├── normalize.py │ └── utils │ ├── __init__.py │ └── hgvs_tools.py ├── submodules └── README.md └── tests ├── cassettes ├── test_data_proxies[rest_dataproxy].yaml ├── test_normalize_allele.yaml └── test_vcrtest.yaml ├── conftest.py ├── data └── seqrepo │ └── latest │ ├── aliases.sqlite3 │ └── sequences │ ├── 2016 │ └── 0824 │ │ └── 050304 │ │ ├── 1472014984.5124342.fa.bgz │ │ ├── 1472014984.5124342.fa.bgz.fai │ │ └── 1472014984.5124342.fa.bgz.gzi │ ├── 2017 │ ├── 1229 │ │ └── 1905 │ │ │ ├── 1514574356.16819.fa.bgz │ │ │ ├── 1514574356.16819.fa.bgz.fai │ │ │ └── 1514574356.16819.fa.bgz.gzi │ └── 1230 │ │ ├── 0059 │ │ ├── 1514595569.2097511.fa.bgz │ │ ├── 1514595569.2097511.fa.bgz.fai │ │ └── 1514595569.2097511.fa.bgz.gzi │ │ └── 0105 │ │ ├── 1514595940.9693692.fa.bgz │ │ ├── 1514595940.9693692.fa.bgz.fai │ │ └── 1514595940.9693692.fa.bgz.gzi │ └── db.sqlite3 ├── extras ├── cassettes │ ├── test_annotate_vcf_grch37_attrs.yaml │ ├── test_annotate_vcf_grch38_attrs.yaml │ ├── test_annotate_vcf_grch38_attrs_altsonly.yaml │ ├── test_annotate_vcf_grch38_noattrs.yaml │ ├── test_annotate_vcf_pickle_only.yaml │ ├── test_annotate_vcf_vcf_only.yaml │ ├── test_from_beacon.yaml │ ├── test_from_gnomad.yaml │ ├── test_from_hgvs.yaml │ ├── test_get_vrs_object_invalid_input.yaml │ ├── test_hgvs[NC_000007.14:g.55181220del-expected2].yaml │ ├── test_hgvs[NC_000007.14:g.55181230_55181231insGGCT-expected3].yaml │ ├── test_hgvs[NC_000007.14:g.55181320A>T-expected1].yaml │ ├── test_hgvs[NC_000013.11:g.32316467dup-expected5].yaml │ ├── test_hgvs[NC_000013.11:g.32331093_32331094dup-expected4].yaml │ ├── test_hgvs[NC_000013.11:g.32936732=-expected0].yaml │ ├── test_hgvs[NC_000019.10:g.289464_289465insCACA-expected8].yaml │ ├── test_hgvs[NC_000019.10:g.289485_289500del-expected9].yaml │ ├── test_hgvs[NM_001331029.1:c.722A>G-expected6].yaml │ ├── test_hgvs[NM_181798.1:c.1007G>T-expected7].yaml │ ├── test_rle_round_trip_gnomad_spdi.yaml │ ├── test_rle_seq_limit.yaml │ ├── test_to_hgvs_iri_ref_keyerror.yaml │ └── test_to_spdi.yaml ├── data │ ├── test_vcf_expected_altsonly_output.vcf.gz │ ├── test_vcf_expected_output.vcf.gz │ ├── test_vcf_expected_output_no_vrs_attrs.vcf.gz │ └── test_vcf_input.vcf ├── test_allele_translator.py ├── test_annotate_vcf.py ├── test_cnv_translator.py └── test_object_store.py ├── test_dataproxy.py ├── test_vcr.py ├── test_vrs.py ├── test_vrs_normalize.py └── validation ├── data ├── test_functions.py ├── test_models.py └── test_schemas.py /.binder/postBuild: 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