├── .github └── workflows │ └── testmac.yml ├── .gitignore ├── .gitmodules ├── .readthedocs.yml ├── .travis.yml ├── CLAUDE.md ├── CMakeLists.txt ├── LICENSE ├── Makefile ├── PYBIND_README.md ├── README.md ├── README_BOTS.md ├── bdsg ├── cmake_bindings │ ├── bdsg.cpp │ ├── bdsg.modules │ ├── bdsg.sources │ ├── bdsg │ │ ├── graph_proxy.cpp │ │ ├── graph_proxy_1.cpp │ │ ├── internal │ │ │ ├── base_packed_graph.cpp │ │ │ ├── eades_algorithm.cpp │ │ │ ├── hash_map.cpp │ │ │ ├── is_single_stranded.cpp │ │ │ ├── mapped_structs.cpp │ │ │ ├── mapped_structs_1.cpp │ │ │ └── wang_hash.cpp │ │ ├── overlays │ │ │ ├── packed_path_position_overlay.cpp │ │ │ ├── packed_reference_path_overlay.cpp │ │ │ ├── path_position_overlays.cpp │ │ │ ├── path_subgraph_overlay.cpp │ │ │ ├── reference_path_overlay.cpp │ │ │ ├── strand_split_overlay.cpp │ │ │ └── vectorizable_overlays.cpp │ │ ├── packed_graph.cpp │ │ └── snarl_distance_index.cpp │ ├── handlegraph │ │ ├── expanding_overlay_graph.cpp │ │ ├── handle_graph.cpp │ │ ├── mutable_path_metadata.cpp │ │ ├── mutable_path_mutable_handle_graph.cpp │ │ ├── path_handle_graph.cpp │ │ ├── path_metadata.cpp │ │ ├── path_position_handle_graph.cpp │ │ ├── trivially_serializable.cpp │ │ └── types.cpp │ └── std │ │ └── bdsg │ │ └── internal │ │ └── binder_hook_bind.cpp ├── docs │ ├── Doxyfile.in │ ├── Makefile │ ├── assets │ │ ├── lil.gfa │ │ └── lil.png │ ├── conf.py │ ├── exampleGraph.pptx │ ├── exdata │ │ ├── cactus-brca2.gfa │ │ ├── cactus-brca2.pg │ │ ├── cactus-brca2.vg │ │ └── graph.pg │ ├── handlegraph.md │ ├── img │ │ ├── exampleGraph.png │ │ ├── exampleGraphPath.png │ │ ├── exampleGraphPath2.png │ │ ├── exampleGraphPath3.png │ │ └── exampleGraphPath4.png │ ├── index.rst │ ├── odgi-presentation-stringology-2019 │ │ ├── 1000GP_wg_log.pdf │ │ ├── H_3136.pdf │ │ ├── Makefile │ │ ├── RPLP0_90_ClustalW_aln.png │ │ ├── TqkY9nw1.png │ │ ├── cactus_yeast.png │ │ ├── cichlid_log.pdf │ │ ├── entropy-19-00299-g003.png │ │ ├── gbwt-example.pdf │ │ ├── igv_graph_realign.png │ │ ├── seqwish_yeast.png │ │ ├── stringology2019.tex │ │ ├── text_variant_graph.jpg │ │ ├── vg_logo.png │ │ ├── vg_tubemap.pdf │ │ ├── w_graph.pdf │ │ ├── wt_ptr_and_non.png │ │ ├── wt_ptr_and_wm.png │ │ └── xg_index_sketch_nice.pdf │ ├── requirements.txt │ └── rst │ │ ├── api.rst │ │ ├── cppapi.rst │ │ ├── glossary.rst │ │ ├── install.rst │ │ └── tutorial.rst ├── include │ └── bdsg │ │ ├── graph_proxy.hpp │ │ ├── hash_graph.hpp │ │ ├── internal │ │ ├── base_packed_graph.hpp │ │ ├── binder_hook_bind.hpp │ │ ├── binder_hook_compile.hpp │ │ ├── dynamic_types.hpp │ │ ├── eades_algorithm.hpp │ │ ├── endianness.hpp │ │ ├── graph_proxy_fragment.classfragment │ │ ├── graph_proxy_handle_graph_fragment.classfragment │ │ ├── graph_proxy_mutable_path_deletable_handle_graph_fragment.classfragment │ │ ├── graph_proxy_path_handle_graph_fragment.classfragment │ │ ├── graph_proxy_serializable_handle_graph_fragment.classfragment │ │ ├── hash_map.hpp │ │ ├── is_single_stranded.hpp │ │ ├── mapped_structs.hpp │ │ ├── packed_structs.hpp │ │ ├── utility.hpp │ │ ├── varint.hpp │ │ └── wang_hash.hpp │ │ ├── overlays │ │ ├── overlay_helper.hpp │ │ ├── packed_path_position_overlay.hpp │ │ ├── packed_reference_path_overlay.hpp │ │ ├── packed_subgraph_overlay.hpp │ │ ├── path_position_overlays.hpp │ │ ├── path_subgraph_overlay.hpp │ │ ├── reference_path_overlay.hpp │ │ ├── strand_split_overlay.hpp │ │ ├── subgraph_overlay.hpp │ │ └── vectorizable_overlays.hpp │ │ ├── packed_graph.hpp │ │ └── snarl_distance_index.hpp └── src │ ├── eades_algorithm.cpp │ ├── hash_graph.cpp │ ├── is_single_stranded.cpp │ ├── mapped_structs.cpp │ ├── packed_graph.cpp │ ├── packed_path_position_overlay.cpp │ ├── packed_reference_path_overlay.cpp │ ├── packed_subgraph_overlay.cpp │ ├── path_position_overlays.cpp │ ├── path_subgraph_overlay.cpp │ ├── reference_path_overlay.cpp │ ├── snarl_distance_index.cpp │ ├── strand_split_overlay.cpp │ ├── subgraph_overlay.cpp │ ├── 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