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Version 0.4.0: June 16, 2026

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.

Version 0.3.0: Dec 9, 2024

General:

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

Version 0.2.9: Oct 28, 2024

General:

• Minor bug fix to createHaplotypeTable for IGH haplotypes

Version 0.2.8: July 29, 2024

General:

• Minor bug fix to createHaplotypeTable for TRB haplotypes

Version 0.2.7: July 2, 2024

General:

• Minor bug fix to createHaplotypeTable

Version 0.2.6: April 26, 2024

General:

• Minor bug fix to hapDendo

Version 0.2.5: February 6, 2023

General:

• Removed deprecated function of dplyr

Version 0.2.4: September 14, 2022

General:

• Generalized the createFullHaplotype to allow other genes as anchor.

Version 0.2.3: March 14, 2022

General:

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

Version 0.2.1: February 16, 2022

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.

Version 0.1.6: June 10, 2020

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.

Version 0.1.5: June 10, 2020

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.

Version 0.1.4: January 28, 2020

• Fixed bug within the hapHeatmap visualization.

Version 0.1.3.999: November 18, 2019

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

Version 0.1.3: September 8, 2019

• Optimized hapHeatmap visualization, r base graph.

Version 0.1.2: July 25, 2019

• Improved visualization of short read sequences annotation.

Version 0.1.1: May 8, 2019

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

Version 0.1.0: March 4, 2019

• Initial public release.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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