GBWT-rs 0.3.0

• gbunzip:
  • Outputs GFA version 1.1.
  • Option for using PanSN path names.
  • Suppors the reference samples header tag RS used by vg.
• Terminology change for compatibility with vg:
  • Paths with sample name _gbwt_ref are now generic named paths.
  • Paths can be promoted to reference paths by specifying sample names in GBWT tag reference_samples.
• New functionality:
  • GBZ::weakly_connected_components for finding weakly connected components in the graph.
  • Functions for determining if an edge or a path is in canonical orientation.

GBWT-rs 0.2.2

Another patch release for the GBZ paper.

• Increase the maximum number of decompression threads in gbunzip from 31 to 64.

GBWT-rs 0.2.1

Minor patch release for the GBZ paper.

• Support for empty paths.
• gbunzip uses Rayon for multithreading.

GBWT-rs 0.2.0

• Graph: GBWTGraph implementation storing node sequences and node-to-segment translation.
• GBZ: Graph interface.
  • Iterators in the original graph: nodes, predecessors/successors of a node, paths over nodes, extensions of a set of paths.
  • Iterators in the GFA graph: segments, predecessors/successors of a segment, paths over segments.
• Interface changes:
  • Runs and GBWT positions use Run and Pos types instead of (usize, usize) pairs.
  • Node / path orientation uses enum Orientation instead of bool.
• Proof-of-concept gbunzip tool for decompressing GFA from GBZ.
  • Somewhat slower than the C++ implementation but supports multi-threaded path extraction for faster decompression.
  • Better parallelization when allowed to reorder the paths opportunistically.

GBWT-rs 0.1.0

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.