Changes in version 1.2.0 (2026-02-17)                  

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:

  - Added: igraph, stringdist, cluster, ape
  - Moved to Suggests: ComplexHeatmap, dplyr, ggtree
  - Removed from Imports: dplyr (replaced with data.table operations)

MINOR CHANGES:

  - Improved CRAN compliance with proper Author and Maintainer fields
  - Added test suite using testthat (edition 3)
  - Redesigned Shiny app with modular architecture
  - Added Conda recipe for bioconda distribution

BUG FIXES:

  - Fixed deprecated dplyr::between() calls
  - Fixed deprecated dplyr::bind_rows() calls
  - Replaced deprecated S4 slot access patterns

                 Changes in version 1.0.7 (2025-04-09)                  

  - Working version for CRAN.

                        Changes in version 1.0.6                        

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

                        Changes in version 1.0.5                        

  - 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.

                        Changes in version 1.0.4                        

  - Fixed bug in download_zenodo_files.

                        Changes in version 1.0.3                        

  - Fixed bug in download_zenodo_files.

                 Changes in version 1.0.1 (2023-08-16)                  

  - Fixed bug in download_zenodo_files.

  - First CRAN release.

                 Changes in version 1.0.0 (2023-06-13)                  

  - First release.

                        Changes in version 0.0.1                        

  - Stable version.