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.
