Documentation:
General:
New Features:
pos_range_max argument to findNovelAlleles and plotNovel. With
pos_range_max, TIgGER takes into account the position in which the V sequence
alignment ends based on the aligner (usually pos_range_max="v_germline_end").
With pos_range_max=NULL, mutation count uses all nucleotides in the IMGT V
region. This means that when the V is trimmed on the 3', TIgGER includes in
the mutation count nucleotides from the CDR3.Bug Fixes:
Updated the error check in positionMutations to check for both empty GERM_NT
positions and absence of IMGT gaps in the germline. Before, gapped germlines
of less than 312 positions ( IGHV4-31*09, 311 positions) would have empty
GERM_NT positions, and the function would stop with an error message
'Check you are using gapped reference germlines'.
Fixed bug in selectNovel where keep_alleles=T would not keep different alleles
leading to the same novel sequence.
Fixed bug genotypeFasta where it wouldn't find duplicate genes.
General:
Replaced error message with warning in function getMutatedAA, to allow for germlines with N (e.g. IGHV1-45*01)
To identify the closest reference, the generateEvidence function will only
consider reference germlines belonging to the same gene segment. This is to
avoid an error when the user provides VDJ references, not just V.
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().