Version 0.4.0 July 18, 2019

Dependencies:

  • 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 0.2.9.999 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 0.2.5.999).

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 0.2.5.999: 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.