Backwards Incompatible Changes:
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.findNovelAlleles are now using lower case (germline_call, not GERMLINE_CALL)General:
AIRRDb.Dependencies:
Bug Fixes:
sortAlleles that was not sorting correctly TR gene names.positionMutations that was counting . as mutated position.New Features:
GermlineIGHV and moved old annotations to SampleGermlineIGHV.v_call), J call (j_call), sequence alignment (seq), junction (junction) and junction length (junction_length) in all functions that use this information.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 -.clip_db to data in findNovelAlleles, plotNovel, inferGenotype and reassignAlleles.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().