gbwt 0.3.0

Partial reimplementation of the GBWT.
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# GBWT-rs releases

## Current version

* New functionality:
  * `GBZ::reference_positions` for finding positions on reference paths for indexing by sequence offsets.
  * GBZ methods for setting reference samples and iterating over them.
  * Longest common subsequence algorithms:
    * `lcs()` for two integer sequences.
    * `path_lcs()` for two paths, weighted by sequence lengths.
    * `fast_weighted_lcs()` for two integer sequences, weighted by an arbitrary function.
  * `GraphPosition` for storing a position in the graph.

## GBWT-rs 0.3.0 (2024-01-29)

* `gbunzip`:
  * Outputs GFA version 1.1.
  * Option for using [PanSN](https://github.com/pangenome/PanSN-spec) 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 (2022-02-22)

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 (2022-02-17)

Minor patch release for the GBZ paper.

* Support for empty paths.
* `gbunzip` uses Rayon for multithreading.

## GBWT-rs 0.2.0 (2021-11-17)

* `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 (2021-09-16)

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.