This release includes automated version bump to 4.4.16, improved release note generation, and refined push workflow. The Makefile has been updated to streamline the release process with new targets for describing, bumping, pushing, and tagging commits. The version.txt and pkg/obioptions/version.go files have been updated to reflect the new version number.
Update GitHub Actions workflow to use setup-go v5 and align with latest tooling practices.
Update version to 4.4.15 in version.txt and pkg/obioptions/version.go.
Add comprehensive documentation for the canonical super-kmer strategy, including:
- Analysis of index v1 limitations
- Experimental observations on super-kmer efficiency
- Detailed pipeline for building v3 index
- Explanation of minimizer-canonization
- Description of unitig construction and frequency filtering
- Storage format specifications for v3
- Aho-Corasick matching implementation
This change introduces a major improvement in index compactness and performance through the use of canonical super-kmers, unitigs, and efficient storage formats.
Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup
This commit introduces Jaccard distance and similarity methods for KmerSet and KmerSetGroup.
For KmerSet:
- Added JaccardDistance method to compute the Jaccard distance between two KmerSets
- Added JaccardSimilarity method to compute the Jaccard similarity between two KmerSets
For KmerSetGroup:
- Added JaccardDistanceMatrix method to compute a pairwise Jaccard distance matrix
- Added JaccardSimilarityMatrix method to compute a pairwise Jaccard similarity matrix
Also includes:
- New DistMatrix implementation in pkg/obidist for storing and computing distance/similarity matrices
- Updated version handling with bump-version target in Makefile
- Added tests for all new methods
