Release Notes¶
Version 1.1.0: October 10, 2023¶
General:
- Updated dependencies to R >= 4.0, alakazam >= 1.3.0, ggplot2 >= 3.4.0, dplyr >= 1.0.0, and tidyr >= 1.1.0 and fixed deprecation warnings. Added utils.
Version 1.0.1: September 19, 2022¶
New Features:
- Added the
pos_range_max
argument tofindNovelAlleles
andplotNovel
. Withpos_range_max
, TIgGER takes into account the position in which the V sequence alignment ends based on the aligner (usuallypos_range_max="v_germline_end"
). Withpos_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
wherekeep_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.
Version 1.0.0: May 12, 2020¶
Backwards Incompatible Changes:
- Changed default expected data format from the Change-O data format to the
AIRR Rearrangement standard. For example, where functions used the column
name
V_CALL
(Change-O) as the default to identify the field that stored the V gene calls, they now usev_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 valuev_call="v_call"
will fail to identify the column with the V gene calls as the columnv_call
doesn’t exist. In this case,v_call="V_CALL"
needs to be specified in the function call. - For consistency with the style of the new data format default, field names in
all other user exposed data structures have been updated to use the same font
case style. e.g, the column names of the results of
findNovelAlleles
are now using lower case (germline_call
, notGERMLINE_CALL
)
General:
- License changed to AGPL-3.
- Added AIRR formatted example data
AIRRDb
. - Updated dependencies to R >= 3.5.0, ggplot2 >= 3.2.0, alakazam >= 1.0.0, shazam >= 1.0.0, and tidyr >=0.1.0.
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 toSampleGermlineIGHV
. - 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-existentv_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 offindNovelAlleles
,inferGenotype
,inferGenotypeBayesian
, andreassignAlleles
. - 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 ofreassignAlleles
to provide options for maintaining reassignments at the gene (previousTRUE
behavior), family, or repertoire level. - Improved tie resolution in
findNovelAlleles
.
Backwards Incompatible Refactors:
- Renamed sample data from
germline_ighv
,sample_db
,genotype
andnovel_df
toGermlineIGHV
,SampleDb
,SampleGenotype
andSampleNovel
, respectively. - Renamed the
novel_df
argument tonovel
inselectNovel
,inferGenotype
, andgenotypeFasta
. - Renamed the
novel_df_row
argument tonovel_row
inplotNovel
. - Argument order in
inferGenotype
was alter for clarity. - Changed the return behavior of
reassignAlleles
so that it returns the input data.frame with theV_CALL_GENOTYPED
column appended or overwritten. cleanSeqs
will no longer replace.
characters with-
.- Renamed
clip_db
todata
infindNovelAlleles
,plotNovel
,inferGenotype
andreassignAlleles
.
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 andfind_unmutated
was set toTRUE
.
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 whennproc
> 1. - Changed default to
nproc=1
infindNovelAlleles()
.
Version 0.2.5: June 07, 2016¶
- Initial CRAN release.