Changes in version 0.4.0 (2026-07-24)                  

New features:

  - convertToASC(): prepare data and germline for haplotype inference
    using PIgLET Allele Similarity Clusters (ASC), resolving duplicated
    genes and aligning with OGRDB reference sets.

Dependencies:

  - Reduced the dependency footprint: removed gtools, RColorBrewer,
    dendextend, rlang and methods; moved plotly, htmlwidgets and
    ggdendro to Suggests (loaded only when needed); moved ggplot2 to
    Imports.

General:

  - Replaced the deprecated ggplot2::aes_string() usage.
  - Added a testthat test suite.
  - Migrated the repository to GitHub with continuous integration and an
    online documentation site.

                        Changes in version 0.3.0                        

General:

  - Minor bug fix to createHaplotypeTable for haplotyping using IGHD
    genes.

                        Changes in version 0.2.9                        

General:

  - Minor bug fix to createHaplotypeTable for IGH haplotypes

                        Changes in version 0.2.8                        

General:

  - Minor bug fix to createHaplotypeTable for TRB haplotypes

                        Changes in version 0.2.7                        

General:

  - Minor bug fix to createHaplotypeTable

                        Changes in version 0.2.6                        

General:

  - Minor bug fix to hapDendo

                 Changes in version 0.2.5 (2023-02-06)                  

General:

  - Removed deprecated function of dplyr

                 Changes in version 0.2.4 (2022-09-22)                  

General:

  - Generalized the createFullHaplotype to allow other genes as anchor.

                        Changes in version 0.2.3                        

General:

  - Fixed a bug in the haplotype plot, cases where a gene is within the
    haplotype table but not in the gene_order flag.

                 Changes in version 0.2.1 (2022-02-16)                  

General:

  - updated the package for changes in dependencies for the haplotype
    plots.
  - add a new function readHaplotypeDb for reading haplotype tables
    created from createFullHaplotype. For tables downloaded from
    VDJbase.org, reading the files into R is recommended with the new
    function.

                        Changes in version 0.1.6                        

Backwards Incompatible Changes:

  - From this version the gene order within plots can be determined by
    the genes_order variable. The variable receives a vector of the
    ordered genes. If not supplied the default order for the genes is by
    the GENE.loc order which can be found in the package using
    data("GENE.loc").
  - Hereby, the gene_order variable has been removed.

General:

  - updated the package for TRB haplotypes.

                 Changes in version 0.1.5 (2020-07-11)                  

Backwards Incompatible Changes:

  - Changed default expected data format from the Change-O data format
    to the AIRR Rearrangement standard. For example, where functions
    used the column name V_CALL (Change-O) as the default to identify
    the field that stored the V gene calls, they now use v_call (AIRR).
    Scripts that relied on default values (previously,
    toHap_col="V_CALL"), will now fail if calls to the functions are not
    updated to reflect the correct value for the data. If data are in
    the Change-O format, the current default value toHap_col="v_call"
    will fail to identify the column with the V gene calls as the column
    v_call doesn't exist. In this case, toHap_col="V_CALL" needs to be
    specified in the function call.
  - For consistency with the style of the new data format default, field
    names in all other user exposed data structures have been updated to
    use the same font case style.

General:

  - Updated dependencies to R >= 3.5.0, dplyr >= 1.0.0, ggplot2
    >= 3.2.0, alakazam >= 1.0.0, tigger >= 1.0.0, and tidyr >=1.0.0.

                 Changes in version 0.1.4 (2020-01-29)                  

  - Fixed bug within the hapHeatmap visualization.

                      Changes in version 0.1.3.999                      

  - Adapted deletionsByVpooled to infer single chromosome deletion from
    light chain repertoire.
  - Added html5 interactive output for deletionHeatmap visualization.

                        Changes in version 0.1.3                        

  - Optimized hapHeatmap visualization, r base graph.

                        Changes in version 0.1.2                        

  - Improved visualization of short read sequences annotation.

                 Changes in version 0.1.1 (2019-05-08)                  

  - Improved createFullHaplotype run-time
  - Fixed a bug wherein createFullHaplotype miss-handled novel allele
    labels

                        Changes in version 0.1.0                        

  - Initial public release.