├── .clang-format ├── .clang-tidy ├── .clangd ├── .dir-locals.el ├── .github ├── actions │ └── setup-gcc │ │ └── action.yml └── workflows │ ├── build_cmake.yml │ ├── macos.yml │ └── test.yml ├── .gitignore ├── .gitmodules ├── .projectile ├── CMakeLists.txt ├── LICENSE ├── README.md ├── app ├── cli │ ├── cli.cpp │ └── cli.hpp ├── main.cpp └── subcommand │ ├── call.cpp │ ├── call.hpp │ ├── decompose.cpp │ ├── decompose.hpp │ ├── gfa2vcf.cpp │ ├── gfa2vcf.hpp │ ├── info.cpp │ └── info.hpp ├── cmake ├── deps.cmake └── sanitizers.cmake ├── docs ├── README.md ├── develop.md ├── refs.md └── vcf.md ├── guix.scm ├── include └── povu │ ├── algorithms │ ├── concealed.hpp │ ├── flubbles.hpp │ ├── midi.hpp │ ├── parallel.hpp │ ├── smothered.hpp │ └── tiny.hpp │ ├── align │ └── align.hpp │ ├── common │ ├── app.hpp │ ├── bounded_queue.hpp │ ├── compat.hpp │ ├── constants.hpp │ ├── core.hpp │ ├── log.hpp │ ├── thread.hpp │ └── utils.hpp │ ├── genomics │ ├── allele.hpp │ ├── genomics.hpp │ ├── graph.hpp │ ├── untangle.hpp │ └── vcf.hpp │ ├── graph │ ├── bidirected.hpp │ ├── bracket_list.hpp │ ├── pvst.hpp │ ├── spanning_tree.hpp │ ├── tree_utils.hpp │ └── types.hpp │ ├── io │ ├── common.hpp │ ├── from_gfa.hpp │ ├── from_pvst.hpp │ ├── to_pvst.hpp │ └── to_vcf.hpp │ ├── overlay │ ├── generic.hpp │ ├── overlay.hpp │ ├── shared.hpp │ └── sne.hpp │ ├── refs │ └── refs.hpp │ └── variation │ ├── color.hpp │ └── rov.hpp ├── src └── povu │ ├── algorithms │ ├── concealed.cpp │ ├── flubbles.cpp │ ├── midi.cpp │ ├── parallel.cpp │ ├── smothered.cpp │ └── tiny.cpp │ ├── align │ └── align.cpp │ ├── common │ ├── thread.cpp │ └── utils.cpp │ ├── genomics │ ├── allele.cpp │ ├── flips.cpp │ ├── genomics.cpp │ ├── graph.cpp │ ├── untangle.cpp │ └── vcf.cpp │ ├── graph │ ├── bidirected.cpp │ ├── bracket_list.cpp │ ├── spanning_tree.cpp │ ├── tree_utils.cpp │ └── types.cpp │ ├── io │ ├── common.cpp │ ├── from_gfa.cpp │ ├── from_pvst.cpp │ ├── to_pvst.cpp │ └── to_vcf.cpp │ ├── overlay │ ├── 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