gbz-base 0.4.0

Pangenome file formats based on SQLite
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# GBZ-base releases

## GBZ-base 0.4.0 (2026-04-17)

* Database versions: GBZ-base v0.4.0, GAF-base version 3
* GBZ-base and GAF-base construction without vg:
  * GBZ-base construction will find top-level chains automatically if not provided.
  * GAF sorting with `gaf_sort()` and the `gafsort` tool.
  * GBWT construction in a background thread when building GAF-base.
* Bug fixes:
  * Exact alignments in a block with varying query lengths are now encoded correctly. GAF-bases must be rebuilt.
* Binaries:
  * Command line arguments can use suffixes (e.g. `k`, `MiB`) for sizes and counts that can plausibly be large.
  * Binaries report peak memory usage.

## GAF-base 0.3.0 (2026-02-18)

* Database versions: GBZ-base v0.4.0, GAF-base version 3
* Support for GBZ version 2 with Zstandard compressed sequences.
* GAF-base version 3:
  * More space-efficient representation of numerical values in table `Alignments`.
  * Database construction parameters stored in table `Tags`.
  * Optional reference-free GAF-base by storing node sequences in table `Nodes`.
  * Option to leave out base quality strings.
  * Also stores unknown optional fields, unless told otherwise.

## GBZ-base 0.2.0 (2025-12-26)

* Database versions: GBZ-base v0.4.0, GAF-base v0.2.0
* `db2gaf` tool for converting a GAF-base back to GAF format.
* Support for [stable graph names](https://github.com/jltsiren/pggname):
  * Uses `pggname::GraphName` for importing graph names and relationships between GBZ tags and GFA/GAF headers.
  * Stable graph names are stored in databases and included in GFA/GAF outputs.
  * `db2gaf` and `query` use the information for determining if the graph is a valid reference for the alignments.

## GBZ-base 0.1.0 (2025-11-06)

* Database versions: GBZ-base v0.4.0, GAF-base v0.2.0

This is the initial release of GBZ-base and GAF-base.

## Release process

* Clean up with `cargo clean`.
* Update database versions to non-dev versions in `db.rs`.
* Update version in `Cargo.toml`.
* Switch to crates.io versions of dependencies, if necessary.
* Update `RELEASES.md`.
* Run `cargo clippy`.
* Run tests with `cargo test`.
* Build documentation with `cargo doc`.
* Build the optimized version with `cargo build --release`.
* Commit the final changes for the release.
* Publish in crates.io with `cargo publish`.
* Push to GitHub.
* Draft a new release in GitHub.