v0.1.0-beta.1

First pre-release v0.1.0-beta.1

After a far too long hiatus, it is time to announce the first official pre-release of jam-rs. This version includes all the basic features for sketching and comparing multiple signatures.

Hashing algorithms

The sketching part includes several configurable algorithms:

• (legacy) Murmurhash3, which produces the same results as other genomic minhashing tools
• xxhash3, a newer algorithm with similar characteristics to murmur3
• Ahash-fallback, an optimised adaptation of the fallback algorithm for small inputs from the Ahash crate. This algorithm is only usable for kmer < 32, but preliminary statistical analysis shows that it produces hashes that are more evenly distributed, with a 3-10x overall speedup compared to xxhash or murmur.

You can choose between two output formats after sketching: sourmash-compatible JSON or a more compact binary representation with additional meta-information. The sourmash-compatible output can be used directly with the regular sourmash pipeline, but note that comparing sketches with non-murmur hashing algorithms will only work if both sides use the same algorithm.

Scaling factors

This tool includes both of the scaling methods from mash and sourmash, plus a combination of both, where a fixed fraction of the hash space is stored, with a fixed lower and/or upper limit per contig. This ensures that all contigs are covered, with the disadvantage of introducing a bias towards smaller (or larger) sequences. This makes it necessary to perform more statistics too make sure that hits do not occur by chance which will follow soon.

What's Changed

• [feat] Feat/hash algs by @St4NNi in #1
• [tests] Feat/refactor tests by @St4NNi in #2
• [0.1.0-beta.1] Feat/compare by @St4NNi in #3

New Contributors

• @St4NNi made their first contribution in #1

Full Changelog: https://github.com/St4NNi/jam-rs/commits/v0.1.0-beta.1

Disclaimer

This is still a pre-release, check it out but take the results with a grain of salt. Additional tests and verifications are in progress and will be released before the final first release.