Releases: St4NNi/jam-rs
v0.1.0-beta.2
First pre-release v0.1.0-beta.2
Same as beta.1, fixes an issue with the binary package on crates.io
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.
You can install it right now via:
> cargo install [email protected]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 sequence. This ensures that all sequences 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
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.
Contributors
Assets 2
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
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.