sourmash-bio/sourmash: v4.2.0
Creators
- C. Titus Brown1
- Luiz Irber2
- Laurent Gautier
- Tim Head3
- Tessa Pierce Ward
- Keya Barve
- Olga Botvinnik4
- Taylor Reiter1
- Erik Young
- Connor Tiffany
- Pranathi Vemuri5
- swamidass
- Phillip Brooks
- Hannah Eve Houts
- Daniel Standage
- Camille Scott6
- Harriet Alexander
- Mohamed Abuelanin1
- Abhishek Anant
- Andreas Sjödin
- Arfon Smith7
- Connor T. Skennerton
- Daniel Dsouza8
- Fabian Klötzl9
- Ivan Ogasawara10
- Katrin Leinweber11
- Marisa Lim12
- Nick
- 1. University of California, Davis
- 2. @10xgenomics
- 3. @BlockSigner
- 4. @czbiohub
- 5. CZ BioHub
- 6. @dib-lab
- 7. @github
- 8. @pqdev
- 9. Profile picture credit goes to XKCD
- 10. xmnlab
- 11. @gitlabhq
- 12. UC Davis
Description
This release adds several significant features: first, we've added a set of taxonomy command-line functionality for combining sourmash gather output with taxonomy databases, and we've also added a new "picklist" feature that enables flexible selection of subsets of databases. Finally, we've added manifests to databases to support picklists as well as faster database loading and signature selection.
As of this release, we've also formally moved development over to the sourmash-bio organization on GitHub, and we've created a new gitter support channel, sourmash-bio/community. Please join us there if you have any questions, comments, or feature requests!
Major new features:
- add
tax/taxonomysubmodule (#1543, #1628, #1630, #1648) - add picklists for subsetting databases and results (#1587, #1588, #1623, #1590, #1639)
- Add manifests to support fast
Index.select(...)and lazy loading (https://github.com/sourmash-bio/sourmash/pull/1590)
Documentation updates:
- Add new GTDB databases description to docs and start legacy databases page (#1581)
- Change
dib-lab/URLs to newsourmash-bio/URLs. (#1629) - Add notice for sustainable open source study (#1580)
Minor new features:
- alias
--nucleotide,--no-nucleotidefor moltype args. (#1632) - add signature names to known/unknown hash sigs output by
sourmash prefetch(#1646)
Bug fixes and performance improvements:
- Speed up
sourmash gatherwith prefetch by ignoring unidentifiable hashes (#1613) - Check for
MinHashcompatibility inMinHash.intersection_and_union(...)(#1627) - Fix selection w/abund and manifest column type conversions (#1645)
Refactoring and cleanup:
- Fix Rust 1.59 lints (#1600)
- Minor cleanup in
sourmash_args&sigsubmodules (#1586) - Minor cleanup in minhash module (#1585)
- Fix needless borrows as suggested by clippy (#1636)
Files
sourmash-bio/sourmash-v4.2.0.zip
Files
(19.9 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/sourmash-bio/sourmash/tree/v4.2.0 (URL)