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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().These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.