reassignAlleles with non-existent v_call column.generateEvidence that was reporting amino acids mutations as NA instead of gaps.Bug Fixes:
reassignAlleles occuring with single match genotypes.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.findNovelAlleles causing overly aggressive minimum sequence threshold filtering.getPopularMutationCount.New Features:
inferGenotypeBayesian function.generateEvidence to build a complete evidence table from the results of findNovelAlleles, inferGenotype, inferGenotypeBayesian, and reassignAlleles.findNovelAlleles and adjusted the definitions/names of some existing columns.keep_gene argument of reassignAlleles to provide options for maintaining reassignments at the gene (previous TRUE behavior), family, or repertoire level.findNovelAlleles.Backwards Incompatible Refactors:
germline_ighv, sample_db, genotype and novel_df to GermlineIGHV, SampleDb, SampleGenotype and SampleNovel, respectively.novel_df argument to novel in selectNovel, inferGenotype, and genotypeFasta.novel_df_row argument to novel_row in plotNovel.inferGenotype was alter for clarity.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 -.findNovelAlleles.inferGenotype would break when performing check for alleles that could not be distinguished.inferGenotype would break if all sequences submitted were from a single gene and find_unmutated was set to TRUE.findNovelAlleles() was not running in parallel, even when nproc > 1.nproc=1 in findNovelAlleles().