.gitignore
.gitmodules
ARCHITECTURE.md
CLAUDE.md
DEVELOPMENT.md
FORMATS.md
Makefile
README.md
RELEASING.md
pyproject.toml
pytest.ini
.github/workflows/release.yml
example-data/README.md
example-data/airr/airr-olmsted-golden.json
example-data/airr/airr-olmsted-golden.json.gz
example-data/airr/input-airr.json
example-data/airr/split-golden-data/clones.test-input-2020.01.30.json
example-data/airr/split-golden-data/datasets.json
example-data/airr/split-golden-data/tree.2a66ad05-bd2f-3e71-a366-ec2f813b4fdf.json
example-data/airr/split-golden-data/tree.330e60ec-22da-3f54-90d6-b6c37d1cb965.json
example-data/airr/split-golden-data/tree.471e8a6d-df0d-3b2e-925f-ee0f534affdd.json
example-data/airr/split-golden-data/tree.6603f069-aa03-3577-a9cd-458dec48f109.json
example-data/airr/split-golden-data/tree.8c67e5fb-a35e-3849-b2f9-c00bfbc8e2c5.json
example-data/airr/split-golden-data/tree.a2b6b304-65d0-324c-809e-fcc29d63882b.json
example-data/airr/split-golden-data/tree.e4439633-0954-32af-9d6b-4cef73af977f.json
example-data/airr/split-golden-data/tree.e5c39dbb-591d-315d-8136-45241236574b.json
example-data/airr/split-golden-data/tree.f0f085a7-57d8-3040-a06b-51be738da83f.json
example-data/fields-config/README.md
example-data/fields-config/config.yaml
example-data/fields-config/input-airr.json
example-data/fields-config/input-olmsted.json
example-data/fields-config/input-pcp.csv
example-data/fields-config/input-trees.csv
example-data/merge/input-mutations.csv
example-data/merge/input-olmsted.json
example-data/merge/merge-olmsted-golden.json
example-data/mutations/input-olmsted.json
example-data/mutations/mutations-config.yaml
example-data/pcp/input-pcp.csv
example-data/pcp/input-trees.csv
example-data/pcp/pcp-olmsted-golden.json
example-data/pcp/pcp-olmsted-golden.json.gz
example-data/pcp-byhand/README.md
example-data/pcp-byhand/input-pcp.csv
example-data/pcp-byhand/input-trees.csv
example-data/pcp-byhand/pcp-byhand-olmsted-golden.json
example-data/pcp-light/input-pcp.csv
example-data/pcp-light/input-trees.csv
example-data/pcp-light/pcp-light-olmsted-golden.json
example-data/pcp-paired/input-pcp.csv
example-data/pcp-paired/input-trees.csv
example-data/pcp-paired/pcp-paired-olmsted-golden.json
example-data/pcp/split-golden-data/clones.dataset-14b429db-6afa-5d76-5c16-dd7dab2897af.json
example-data/pcp/split-golden-data/datasets.json
example-data/pcp/split-golden-data/tree.tree-0439a72b-ba3b-8f9c-b110-04b80e2b9f95.json
example-data/pcp/split-golden-data/tree.tree-0c29513f-8d41-8df5-ac4c-443d4871fe23.json
example-data/pcp/split-golden-data/tree.tree-0e14038f-ac80-8a35-ebb7-2c1b76345a46.json
example-data/pcp/split-golden-data/tree.tree-1009d173-85e1-5593-e2ec-8a895954ecab.json
example-data/pcp/split-golden-data/tree.tree-122c6f7f-bd3e-46f6-0113-bb7303ccdfef.json
example-data/pcp/split-golden-data/tree.tree-1f9dbf6c-d601-bcfa-ec02-57c72ee6a2e9.json
example-data/pcp/split-golden-data/tree.tree-27f6563d-c175-8e5c-5226-a27d4e4b3876.json
example-data/pcp/split-golden-data/tree.tree-2cea4fb5-578e-13af-c10b-350fff8f29a3.json
example-data/pcp/split-golden-data/tree.tree-2e1ba22a-698b-b8a4-c360-0edfaf1a76d8.json
example-data/pcp/split-golden-data/tree.tree-376d1d56-79ef-60c2-7b62-3d2ef11be6cb.json
example-data/pcp/split-golden-data/tree.tree-3ebb9203-9734-6dee-aa6c-0abe8e8f690d.json
example-data/pcp/split-golden-data/tree.tree-4b9ac338-8bbc-6669-41e6-face81dae39b.json
example-data/pcp/split-golden-data/tree.tree-4c247208-9d1c-b8f1-5aa4-5bf50526b6fe.json
example-data/pcp/split-golden-data/tree.tree-4e789983-4517-bda3-11cf-1d3f636ac5dc.json
example-data/pcp/split-golden-data/tree.tree-522fac7a-4689-e49a-05d1-9353af02f885.json
example-data/pcp/split-golden-data/tree.tree-5397d15f-ff5d-f373-c644-e50ae70d4757.json
example-data/pcp/split-golden-data/tree.tree-5d82ca72-029f-eb0a-694b-97f7c2233755.json
example-data/pcp/split-golden-data/tree.tree-638d3467-4353-f020-3b8d-cde69a574892.json
example-data/pcp/split-golden-data/tree.tree-653a97b8-1c82-d1bb-f23b-61dd1f5f95dc.json
example-data/pcp/split-golden-data/tree.tree-654906d9-16e2-5db5-4643-0490059032c0.json
example-data/pcp/split-golden-data/tree.tree-684cf07a-9267-14a4-86ef-7f22aa22d934.json
example-data/pcp/split-golden-data/tree.tree-774e66d4-afbe-0c43-a9f8-a772fcb2ef6c.json
example-data/pcp/split-golden-data/tree.tree-a374a336-cf46-e293-6442-a706dd45bf92.json
example-data/pcp/split-golden-data/tree.tree-ad6976d4-8d00-af56-c046-6ef80924812f.json
example-data/pcp/split-golden-data/tree.tree-c3e192a2-1a85-2141-6fd5-9ab9c29fe5af.json
example-data/pcp/split-golden-data/tree.tree-cc42c52c-6fb9-faa8-b57f-3933f1ac3d30.json
example-data/pcp/split-golden-data/tree.tree-d5df516b-827f-c8de-339b-2b9b1d1e8d08.json
example-data/pcp/split-golden-data/tree.tree-f1f94793-7e38-164c-9c47-024cfc1a9019.json
olmsted_cli/__init__.py
olmsted_cli/api.py
olmsted_cli/build_config.py
olmsted_cli/cli.py
olmsted_cli/column_resolution.py
olmsted_cli/constants.py
olmsted_cli/data_io.py
olmsted_cli/field_metadata.py
olmsted_cli/identifier.py
olmsted_cli/merge.py
olmsted_cli/merge_mutations.py
olmsted_cli/metrics.py
olmsted_cli/process_airr_data.py
olmsted_cli/process_cft_data.py
olmsted_cli/process_data.py
olmsted_cli/process_pcp_data.py
olmsted_cli/process_utils.py
olmsted_cli/schemas.py
olmsted_cli/split.py
olmsted_cli/streaming.py
olmsted_cli/summary.py
olmsted_cli/tag.py
olmsted_cli/types.py
olmsted_cli/utils.py
olmsted_cli/validate.py
olmsted_cli/version.py
olmsted_cli.egg-info/PKG-INFO
olmsted_cli.egg-info/SOURCES.txt
olmsted_cli.egg-info/dependency_links.txt
olmsted_cli.egg-info/entry_points.txt
olmsted_cli.egg-info/requires.txt
olmsted_cli.egg-info/top_level.txt
olmsted_cli/configs/__init__.py
olmsted_cli/configs/templates/fields_header.yaml
olmsted_cli/configs/templates/header.yaml
olmsted_cli/configs/templates/options_airr.yaml
olmsted_cli/configs/templates/options_olmsted.yaml
olmsted_cli/configs/templates/options_pcp.yaml
olmsted_cli/configs/templates/skip_header.yaml
scripts/benchmark_batch_memory.py
tests/__init__.py
tests/conftest.py
tests/test_batching_airr.py
tests/test_batching_mutations.py
tests/test_batching_pcp.py
tests/test_branch_lengths.py
tests/test_build_config.py
tests/test_cli_processing.py
tests/test_clone_group_iterators.py
tests/test_column_resolution.py
tests/test_config.py
tests/test_data_io.py
tests/test_field_metadata.py
tests/test_format_detection.py
tests/test_gzip_io.py
tests/test_identifier.py
tests/test_merge.py
tests/test_merge_fixture.py
tests/test_multi_tree.py
tests/test_output_shape.py
tests/test_pcp_extras.py
tests/test_pcp_multi_tree.py
tests/test_streaming.py
tests/test_streaming_uniqueness.py
tests/test_tag.py
tests/test_uniqueness.py
tests/test_validation.py
tests/golden/build_config/airr.yaml
tests/golden/build_config/olmsted.yaml
tests/golden/build_config/pcp.yaml