NEWS

Version 1.2.0: Feb 2026

MAJOR CHANGES:

Leiden Community Detection: Added support for Leiden algorithm as an alternative to hierarchical clustering. Use clustering_method = "leiden" in inferAlleleClusters(). This is particularly useful for D and J segments with variable-length sequences.
Generalized Distance Functions: The new igDistance() function supports multiple distance calculation methods:
- “decipher”: DECIPHER-based distance (default, best for aligned V segments)
- “hamming”: Hamming distance (requires equal-length sequences)
- “lv”: Levenshtein distance (handles variable-length sequences, good for D/J)
Multi-locus Support: inferAlleleClusters() now explicitly supports all V/D/J segments with the locus parameter.
New Visualization Functions:
- plotTruncatedTree(): Publication-quality circular tree with collapsed subgroups
- plotCommunityNetwork(): Network visualization of cluster relationships
- plotSilhouetteOptimization(): Resolution parameter optimization plot
- plotClusterComparison(): Compare hierarchical and Leiden clustering results

CLASS SYSTEM CHANGES:

S4 to S3 Migration: GermlineCluster is now an S3 class instead of S4.
- Access slots with $ instead of @ (e.g., result$alleleClusterTable)
- Added print(), summary(), and plot() S3 methods
- New slots: clusteringMethod, communityObject, graphObject, distanceMatrix, silhouetteScore, resolutionParameter, locus

API CHANGES:

ighvDistance() is deprecated in favor of igDistance() (backward compatible wrapper provided)
ighvClust() is deprecated in favor of igClust() (backward compatible wrapper provided)
inferAlleleClusters() has new parameters but maintains backward compatibility

DEPENDENCIES:

MINOR CHANGES:

BUG FIXES:

An asc_annotation flag was added to inferGenotypeAllele to simplify genotype by asc annotation.

New Feature! We added a confidence level to genotype inference genotype_confidence.

The confidence is calculated as the Z score of the allele count, repertoire depth, and the allele absolute threshold.