This is a Rust reimplementation of parts of the GBWT and the GBWTGraph. It is based on the Simple-SDS library.
.cargo/config.toml sets the target CPU to native.Various improvements to the gbunzip tool:
* for P-line overlaps.-p / --paths MODE):
default: Named / reference paths as P-lines, other paths as W-lines.pan-sn: All paths as P-lines with PanSN names.ref-only: Named / reference paths as P-lines, no other paths.The gbunzip tool can decompress a GBZ graph into a GFA file. There are some differences to the decompression in the C++ implementation:
-p / --path-order, which can be slower.Added several path-based iterators to GBZ:
path(): over the nodes on the given path.segment_path(): over the segments on the given path.follow_forward(): over forward extensions of a search state.follow_backward(): over backward extensions of a search state.Additionally, runs and GBWT positions now use Run and Pos types instead of (usize, usize) pairs.
Basic support for the GBZ file format:
Also started using proper data types for GFA segments and node/segment/path orientation.
Minimal support for GBWTGraph. Unlike in the original implementation, the GBWTGraph structure only deals with sequences and segments. Operations based on nodes, edges, and links will be implemented in the GBZ structure.
Another patch release for the GBZ paper.
gbunzip from 31 to 64.Minor patch release for the GBZ paper.
gbunzip uses Rayon for multithreading.Graph: GBWTGraph implementation storing node sequences and node-to-segment translation.GBZ: Graph interface.
Run and Pos types instead of (usize, usize) pairs.enum Orientation instead of bool.gbunzip tool for decompressing GFA from GBZ.
This is a reimplementation of some parts of the GBWT and the GBWTGraph in Rust. At the moment, the main purpose is ensuring that the Simple-SDS file format specifications are complete enough. I may use this in future projects, but at the moment everything can change without warning.
The first pre-release includes supports the GBWT Simple-SDS file format as well as path navigation, unidirectional/bidirectional search, and GBWT metadata. The next version will probably support GBWTGraph, the GBZ format, and GFA extraction.
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