├── .gitattributes ├── .github ├── odgi.sh ├── tap-matcher.json └── workflows │ ├── build.yml │ ├── code-quality.yml │ ├── docs.yml │ └── flatgfa-py.yml ├── .gitignore ├── .zed └── settings.json ├── Cargo.lock ├── Cargo.toml ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── bench ├── .gitignore ├── Makefile ├── bar.vl.json ├── bench.py ├── config.toml ├── graphs.toml ├── sizes.py └── summary.py ├── flatgfa-py ├── .gitignore ├── Cargo.toml ├── README.md ├── docs │ ├── Makefile │ ├── conf.py │ └── index.rst ├── examples │ ├── depth.py │ └── gaf.py ├── flatgfa.pyi ├── pyproject.toml ├── src │ └── lib.rs └── test │ ├── test_flatgfa.py │ ├── test_gaf.py │ ├── tiny.gaf │ └── tiny.gfa ├── flatgfa ├── Cargo.toml ├── README.md ├── src │ ├── cli │ │ ├── cmds.rs │ │ ├── main.rs │ │ └── mod.rs │ ├── file.rs │ ├── flatbed.rs │ ├── flatgfa.rs │ ├── gfaline.rs │ ├── lib.rs │ ├── memfile.rs │ ├── namemap.rs │ ├── ops │ │ ├── bench.rs │ │ ├── chop.rs │ │ ├── depth.rs │ │ ├── extract.rs │ │ ├── gaf.rs │ │ ├── mod.rs │ │ └── position.rs │ ├── packedseq.rs │ ├── parse.rs │ ├── pool.rs │ └── print.rs └── tests │ ├── test.t │ └── turnt.toml ├── mygfa ├── .gitignore ├── README.md ├── docs │ ├── Makefile │ ├── conf.py │ └── index.rst ├── example.py ├── mygfa │ ├── __init__.py │ ├── __main__.py │ ├── gfa.py │ └── preprocess.py └── pyproject.toml ├── pollen_data_gen ├── pollen_data_gen │ ├── __init__.py │ ├── __main__.py │ ├── depth.py │ └── simple.py └── pyproject.toml ├── pollen_icon.png ├── pollen_icon_transparent.png ├── pollen_py ├── README.md ├── pollen │ ├── __init__.py │ ├── argparse_custom.py │ ├── depth │ │ ├── calyx_depth.py │ │ ├── main.py │ │ ├── parse_data.py │ │ ├── processing-elements │ │ │ ├── calyx_depth_simple.py │ │ │ └── parse_data.py │ │ └── python_depth.py │ └── main.py └── pyproject.toml ├── process.py ├── pyproject.toml ├── pyrightconfig.json ├── slow_odgi ├── Makefile ├── README.md ├── pyproject.toml └── slow_odgi │ ├── __init__.py │ ├── __main__.py │ ├── chop.py │ ├── crush.py │ ├── degree.py │ ├── depth.py │ ├── flatten.py │ ├── flip.py │ ├── inject.py │ ├── inject_setup.py │ ├── matrix.py │ ├── norm.py │ ├── overlap.py │ ├── paths.py │ ├── proofs.py │ ├── somepaths.py │ ├── validate.py │ └── validate_setup.py ├── tests ├── .gitignore ├── basic │ ├── ex1.gfa │ └── ex2.gfa ├── depth │ ├── basic │ │ ├── ex1.gfa │ │ └── ex2.gfa │ ├── subset-paths │ │ ├── ex1.paths │ │ ├── ex1.txt │ │ ├── ex2.paths │ │ ├── ex2.txt │ │ └── turnt.toml │ └── turnt.toml ├── handmade │ ├── crush1.gfa │ ├── flip1.gfa │ ├── flip2.gfa │ ├── flip3.gfa │ └── no-test-flip4.gfa ├── subset-paths │ ├── ex1.paths │ ├── ex1.txt │ ├── ex2.paths │ └── ex2.txt └── turnt.toml └── uv.lock /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cucapra/pollen/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/odgi.sh: 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