Version 1.0.1: September 19, 2022
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New Features:
+ Added the `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.
Version 1.0.0: May 12, 2020
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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 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.
+ 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`, not `GERMLINE_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
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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 to `SampleGermlineIGHV`.
+ 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
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+ Fixed a fatal error in `reassignAlleles` with non-existent `v_call` column.
+ Fixed bug in `generateEvidence` that was reporting amino acids mutations as
NA instead of gaps.
Version 0.3.0 October 3, 2018
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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 of `findNovelAlleles`, `inferGenotype`,
`inferGenotypeBayesian`, and `reassignAlleles`.
+ 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 of `reassignAlleles` to provide
options for maintaining reassignments at the gene (previous `TRUE` behavior),
family, or repertoire level.
+ Improved tie resolution in `findNovelAlleles`.
Backwards Incompatible Refactors:
+ Renamed sample data from `germline_ighv`, `sample_db`, `genotype` and
`novel_df` to `GermlineIGHV`, `SampleDb`, `SampleGenotype` and `SampleNovel`,
respectively.
+ Renamed the `novel_df` argument to `novel` in `selectNovel`, `inferGenotype`,
and `genotypeFasta`.
+ Renamed the `novel_df_row` argument to `novel_row` in `plotNovel`.
+ Argument order in `inferGenotype` was alter for clarity.
+ Changed the return behavior of `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 `-`.
+ Renamed `clip_db` to `data` in `findNovelAlleles`, `plotNovel`,
`inferGenotype` and `reassignAlleles`.
Version 0.2.11 September 21, 2017
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+ Improved memory utilization in `findNovelAlleles`.
Version 0.2.10 July 1, 2017
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+ Bugfix wherein `inferGenotype` would break when performing check for alleles
that could not be distinguished.
Version 0.2.9.999 May 16, 2017
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+ Bugfix wherein `inferGenotype` would break if all sequences submitted were
from a single gene and `find_unmutated` was set to `TRUE`.
Version 0.2.9: March 24, 2017
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+ License changed to Creative Commons Attribution-ShareAlike 4.0 International
(CC BY-SA 4.0).
Version 0.2.8: August 26, 2016
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+ 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
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+ 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
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+ Updated code to work with the latest version of dplyr (0.5.0).
Version 0.2.5.999: June 10, 2016
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+ Fixed a bug werein `findNovelAlleles()` was not running in parallel, even
when `nproc` > 1.
+ Changed default to `nproc=1` in `findNovelAlleles()`.
Version 0.2.5: June 07, 2016
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+ Initial CRAN release.