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.
Update version from 4.4.11 to 4.4.12
- Bump version in version.go
- Enhance release note generation in Makefile to use JSON output from orla and fallback to raw output if JSON parsing fails
- Improve test script to verify minimum super k-mer length is >= k (default k=31)
Mise à jour du Makefile pour améliorer le processus de version bump et de création de tag.
- Utilisation de variables pour stocker les versions précédente et actuelle
- Ajout de la génération automatique des notes de version à partir des commits entre les tags
- Intégration d'une logique de fallback si orla n'est pas disponible
- Amélioration de la documentation des étapes du processus de release
- Mise à jour de la commande de création du tag avec le message généré
This commit introduces a new GitHub Actions workflow to automatically create releases when tags matching the pattern 'Release_*' are pushed. It also updates the Makefile to use the new tag format 'Release_<version>' for tagging commits, ensuring consistency with the new release automation.
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
