This commit refactors the k-mer index management tools to use a unified subcommand structure with obik, adds support for per-set metadata and ID management, enhances the k-mer set group builder to support appending to existing groups, and improves command-line option handling with a new global options registration system.
Key changes:
- Introduce obik command with subcommands (index, ls, summary, cp, mv, rm, super, lowmask)
- Add support for per-set metadata and ID management in kmer set groups
- Implement ability to append to existing kmer index groups
- Refactor option parsing to use a global options registration system
- Add new commands for listing, copying, moving, and removing sets
- Enhance low-complexity masking with new options and output formats
- Improve kmer index summary with Jaccard distance matrix support
- Remove deprecated obikindex and obisuperkmer commands
- Update build process to use the new subcommand structure
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
This commit refactors the k-mer normalization functions, renaming them from 'NormalizeKmer' to 'CanonicalKmer' to better reflect their purpose of returning canonical k-mers. It also introduces new quorum operations (AtLeast, AtMost, Exactly) for k-mer set groups, along with comprehensive tests and benchmarks. The version commit hash has also been updated.
Ajout de la fonctionnalité de sauvegarde et de chargement pour FrequencyFilter en utilisant le KmerSetGroup sous-jacent.
- Nouvelle méthode Save() pour enregistrer le filtre dans un répertoire avec formatage des métadonnées
- Nouvelle méthode LoadFrequencyFilter() pour charger un filtre depuis un répertoire
- Initialisation des métadonnées lors de la création du filtre
- Optimisation des méthodes Union() et Intersect() du KmerSetGroup
- Mise à jour du commit hash
This commit refactors all k-mer encoding and normalization functions to consistently use 'canonical' instead of 'normalized' terminology. This includes renaming functions like EncodeNormalizedKmer to EncodeCanonicalKmer, IterNormalizedKmers to IterCanonicalKmers, and NormalizeKmer to CanonicalKmer. The change aligns the API with biological conventions where 'canonical' refers to the lexicographically smallest representation of a k-mer and its reverse complement. All related documentation and examples have been updated accordingly. The commit also updates the version file with a new commit hash.
This commit introduces new functions for encoding and decoding k-mers, including support for normalized k-mers. It also updates the frequency filter and k-mer set implementations to use the new encoding functions, providing zero-allocation encoding for better performance. The commit hash has been updated to reflect the latest changes.
This commit refactors the KmerSet and related structures to use an immutable K parameter and introduces consistent Copy methods instead of Clone. It also adds attribute API support for KmerSet and KmerSetGroup, and updates persistence logic to handle IDs and metadata correctly.
Cette modification ajoute la capacité de stocker et de persister des métadonnées utilisateur dans les structures KmerSet et KmerSetGroup. Les changements incluent l'ajout d'un champ Metadata dans KmerSet et KmerSetGroup, ainsi que la mise à jour des méthodes de clonage et de persistance pour gérer ces métadonnées. Cela permet de conserver des informations supplémentaires liées aux ensembles de k-mers tout en maintenant la compatibilité avec les opérations existantes.
This commit adds support for saving and loading KmerSet and KmerSetGroup structures using TOML, YAML, and JSON formats for metadata. It includes:
- Added github.com/pelletier/go-toml/v2 dependency
- Implemented Save and Load methods for KmerSet and KmerSetGroup
- Added metadata persistence with support for multiple formats (TOML, YAML, JSON)
- Added helper functions for format detection and metadata handling
- Updated version commit hash
This commit refactors the k-mer encoding logic to handle ambiguous bases more consistently and introduces a KmerSet type for better management of k-mer collections. The frequency filter now works with KmerSet instead of roaring bitmaps directly, and the API has been updated to support level-based frequency queries. Additionally, the commit updates the version and commit hash.
This commit introduces error handling for ambiguous DNA bases (N, R, Y, W, S, K, M, B, D, H, V) in k-mer encoding. It adds new functions IterNormalizedKmersWithErrors and EncodeNormalizedKmersWithErrors that track and encode the number of ambiguous bases in each k-mer using error markers in the top 2 bits. The commit also updates the version string to reflect the latest changes.
Ajout d'une fonctionnalité pour le filtrage unique qui prend en compte à la fois la séquence et les catégories.
- Modification de la fonction ISequenceChunk pour accepter un classifieur unique optionnel
- Implémentation du traitement unique sur disque en utilisant un classifieur composite
- Mise à jour du classifieur utilisé pour le tri sur disque
- Correction de la gestion des clés de unicité en utilisant le code et la valeur du classifieur
- Mise à jour du numéro de commit
