Version 1.0.0: May 12, 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, v_call="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 v_call="v_call" will fail to identify the column with the V gene calls as the column v_call doesn’t exist. In this case, v_call="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. e.g, the column names of the results of findNovelAlleles are now using lower case (germline_call, not GERMLINE_CALL)


  • License changed to AGPL-3.
  • Added AIRR formatted example data AIRRDb.
  • Updated dependencies to R >= 3.5.0, ggplot2 >= 3.2.0, alakazam >= 1.0.0, shazam >= 1.0.0, and tidyr >=0.1.0.

Version 0.4.0 July 18, 2019


  • Upgraded to alakazam >= 0.3.0, shazam >= 0.2.0, dplyr >= 0.8.1 and ggplot2 >= 3.1.1

Bug Fixes:

  • Fixed bug in sortAlleles that was not sorting correctly TR gene names.
  • Fixed bug in positionMutations that was counting . as mutated position.

New Features:

  • Updated IGHV germline gene segment alleles in GermlineIGHV and moved old annotations to SampleGermlineIGHV.
  • Added the option to specify with arguments the names of the columns that contain V call (v_call), J call (j_call), sequence alignment (seq), junction (junction) and junction length (junction_length) in all functions that use this information.

Version 0.3.1 October 19, 2018

  • Fixed a fatal error in reassignAlleles with non-existent v_call column.
  • Fixed bug in generateEvidence that was reporting amino acids mutations as NA instead of gaps.

Version 0.3.0 October 3, 2018

Bug Fixes:

  • Fixed a bug in reassignAlleles occuring with single match genotypes.
  • Fixed selectNovel improperly removing all identical novel alleles, rather than keeping a single entry.
  • genotypeFasta will now retain IMGT-numbering spacers as . characters instead of converting them to - characters.
  • Fixed a bug in findNovelAlleles causing overly aggressive minimum sequence threshold filtering.
  • Fixed a bug in the grouping behavior of getPopularMutationCount.

New Features:

  • Added a Bayesian approach to genotype inferrence as the inferGenotypeBayesian function.
  • Added the function generateEvidence to build a complete evidence table from the results of findNovelAlleles, inferGenotype, inferGenotypeBayesian, and reassignAlleles.
  • Added multiple new evidence columns to the output of findNovelAlleles and adjusted the definitions/names of some existing columns.
  • Added behavior to the keep_gene argument of reassignAlleles to provide options for maintaining reassignments at the gene (previous TRUE behavior), family, or repertoire level.
  • Improved tie resolution in findNovelAlleles.

Backwards Incompatible Refactors:

  • Renamed sample data from germline_ighv, sample_db, genotype and novel_df to GermlineIGHV, SampleDb, SampleGenotype and SampleNovel, respectively.
  • Renamed the novel_df argument to novel in selectNovel, inferGenotype, and genotypeFasta.
  • Renamed the novel_df_row argument to novel_row in plotNovel.
  • Argument order in inferGenotype was alter for clarity.
  • Changed the return behavior of reassignAlleles so that it returns the input data.frame with the V_CALL_GENOTYPED column appended or overwritten.
  • cleanSeqs will no longer replace . characters with -.
  • Renamed clip_db to data in findNovelAlleles, plotNovel, inferGenotype and reassignAlleles.

Version 0.2.11 September 21, 2017

  • Improved memory utilization in findNovelAlleles.

Version 0.2.10 July 1, 2017

  • Bugfix wherein inferGenotype would break when performing check for alleles that could not be distinguished.

Version May 16, 2017

  • Bugfix wherein inferGenotype would break if all sequences submitted were from a single gene and find_unmutated was set to TRUE.

Version 0.2.9: March 24, 2017

  • License changed to Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0).

Version 0.2.8: August 26, 2016

  • Bugfix following recent update of alakazam (0.2.5) to import selectively.
  • Removed unneeded dependency on shazam package (not needed as of

Version 0.2.7: July 24, 2016

  • More updates to work with the latest version of dplyr (0.5.0).
  • Bugfix in findNovelAlleles when allele passed germline_min but not min_seqs.
  • Fixed vignette typo and updated findUnmutatedCalls man page.

Version 0.2.6: July 01, 2016

  • Updated code to work with the latest version of dplyr (0.5.0).

Version June 10, 2016

  • Fixed a bug werein findNovelAlleles() was not running in parallel, even when nproc > 1.
  • Changed default to nproc=1 in findNovelAlleles().

Version 0.2.5: June 07, 2016

  • Initial CRAN release.