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gbwt-rs
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GBZ file format for pangenome graphs
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gbwt-rs
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# GBZ file format for pangenome graphs This is a Rust reimplementation of parts of the [GBWT](https://github.com/jltsiren/gbwt) and the [GBWTGraph](https://github.com/jltsiren/gbwtgraph). It is based on the [Simple-SDS](https://github.com/jltsiren/simple-sds) library. ## Scope ### GBWT - [x] Simple-SDS [file format](https://github.com/jltsiren/gbwt/blob/master/SERIALIZATION.md) - [x] Iteration over paths - [x] Unidirectional search - [x] Bidirectional search - [x] Metadata - [x] Construction - [ ] Locate queries ### GBZ - [x] Simple-SDS [file format](https://github.com/jltsiren/gbwtgraph/blob/master/SERIALIZATION.md) - [x] Iteration over nodes and edges - [x] Iteration over segments and links - [x] Iteration over paths and path extensions - [x] GFA extraction ### Possible future extensions * GBWT/GBZ merging * Cached GBWT ## Notes * The included `.cargo/config.toml` sets the target CPU to `native`. * See [Simple-SDS](https://github.com/jltsiren/simple-sds) for assumptions on the environment.
