                 Changes in version 3.1.0 (2026-04-30)                  

    o   Removed reference to http://tools.immunogenomics.org from the DESCRIPTION.

    o   Added the Data.Type parameter to the BIGDAWG() function to identify the 'motif' data type.

    o   Added Livia Tran as a package author.

                        Changes in version 3.0.9                        

    o   Fixed "conditon has length >1" error in R v4.2+. Thanks to Ryan Chung for the report.

    o   Removed httr from Imports

    o   Updated URL to 'HLA Nomenclature Naming Alleles' page at hla.alleles.org

    o   Updated email address in vignette

                        Changes in version 3.0.8                        

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.53, 2023-07)

                        Changes in version 3.0.7                        

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.52.0, 2023-04)

    o   Bug fix for certain data tables

                        Changes in version 3.0.6                        

    o   Adjustment for data table read-ins

    o   Name change in an IMGT/HLA file

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.50.0, 2022-10)

    o   Calculation adjustment for Odds Ratio Tables. Thanks to Ben Solomon.

                        Changes in version 3.0.5                        

    o   Bug identified when using EVS.rm = T

                        Changes in version 3.0.4                        

    o   Bug identified when using R > v4.1

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.49, 2022-07).

    o   Adjustment to A test for reporting to file

                 Changes in version 3.0.3 (2021-11-17)                  

    o   Removed invariant positions from amino analysis output

    o   Minor formatting changes to output files

    o   Change to CheckRelease based on remote file updates

    o   Differentiate invariant AA positions from invalid AA positions for chisq

                        Changes in version 3.0.2                        

    o   Added export of Exon to parameters file

                        Changes in version 3.0.1                        

    o   Adjustment to targeted exon specific amino acid analysis alignment filter

    o   Added known issues section to BIGDAWG vignette

                        Changes in version 3.0.0                        

    o   Allows for targeted exon specific amino acid analysis, Exon argument

                        Changes in version 2.5.4                        

    o   Adjustment to amino acid analysis frequency calculator

    o   Few grammatical fixes

                        Changes in version 2.5.3                        

    o   Adjustment to amino acid analysis frequency calculator

    o   Few grammatical fixes

                        Changes in version 2.5.2                        

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.46 (2021-10) Build 6c613ce).

    o   Removed p-group reduction for amino acid aligment analysis.

                        Changes in version 2.5.1                        

    o   Check defined Loci.Set against data.

    o   Few organizational chances to amino acid analysis. No change to functionality.

    o   Few grammatical fixes

                         Changes in version 2.5                         

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.45.1, 2021-07-12).

    o   Small bug fix in binning algorithm

                         Changes in version 2.4                         

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.44.0, 2021-04-20).

    o   BIGDAWG now utilizes full length protein sequences (future plan to be exon specific).

    o   Small bug fix in binning algorithm

                 Changes in version 2.3.6 (2021-02-11)                  

    o   Bug in contextual binning algorithm

    o   Error messages redirected to Std Err.

                        Changes in version 2.3.5                        

    o   Release v2.3.5 restricted to internal releases

    o   Adjustment to contextual binning algorithm

                        Changes in version 2.3.4                        

    o   Release v2.3.4 restricted to internal releases

    o   Adjustment of contextual binning algorithm

    o   Fixed bug introduced in L test freq calculations

                        Changes in version 2.3.3                        

    o   Release v2.3.3 restricted to internal releases

    o   Rework of contextual binning sort and output

                        Changes in version 2.3.2                        

    o   Release v2.32.2 restricted to internal releases

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.43.0, 2021-01-18).

    o   Fixed bug in counting for some tables with NA values.

    o   Fixed bug in protein alignment generation.

    o   Minor code adjust to CheckRelease() and UpdateRelease() functions.

    o   Added contextual binning to chi square function (Strict.Bin argument).

                 Changes in version 2.3.1 (2020-10-08)                  

    o   Resubmitted for unarchiving from CRAN.

                  Changes in version 2.3 (2019-11-12)                   

    o   Changes to NEWS format

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.38.0, 2019-10-17).

                        Changes in version 2.2.1                        

    o   Fixed bug where passed R object exports to parameter file.

    o   Small changes to console output.

                         Changes in version 2.2                         

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.33.0, 2018-07-11).

                        Changes in version 2.1.4                        

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.32.0, 2018-04-16).

    o   Small code fix for updating exon alignment to latest release

                        Changes in version 2.1.3                        

    o   CheckAllele bug when Trim=T and Res=1 or with 1-Field (2-digit) data.

                        Changes in version 2.1.2                        

    o   Haplotype ChiSq output bug fix when All.Pairwise=T.

                        Changes in version 2.1.1                        

    o   GLS to table conversion bug fix - GLSconvert(..,type=GL2Tab).

                  Changes in version 2.1 (2018-02-08)                   

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.31.0, 2018-01-19).

                        Changes in version 2.0.2                        

    o   Minor code adjust to CheckRelease() and UpdateRelease() functions.

                        Changes in version 2.0.1                        

    o   BUG Fix thanks to Rajesh Acharya.

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.30.0, 2017-10-27).

    o   Added dependency for httr package.

                         Changes in version 2.0                         

    o   Code re-structuring.

    o   The ability to use Gene List Strings via conversion utility, GLSconvert().

    o   Added GLSconvert Vignette.

                  Changes in version 1.16 (2017-09-06)                  

    o   Submission to CRAN

    o   Some code re-structuring.

    o   Added parameter check function.

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.29.0.1, 2017-08-18).

                       Changes in version 1.15.3                        

    o   Now Data argument accepts properly formatted R dataframes (Data=foo).

                       Changes in version 1.15.2                        

    o   Release v1.15.1 restricted to internal releases.

    o   Fixed miscellaneous bugs specific to HLA data processing.

    o   Now allows for .1, .2, _1, and _2 in column names.

    o   Updates to vignette.

                        Changes in version 1.15                         

    o   Fixed miscellaneous bugs specific to HLA data processing.

    o   Minor adjustments to code for organization and clarity.

                 Changes in version 1.14.2 (2017-07-19)                 

    o   Fixed bug where allele names with '00' would be eroneously changed.

                       Changes in version 1.14.1                        

    o   Minor adjustments to code for organization and clarity.

    o   Fixed bug where sample IDs were not exporting with subject haplotypes. However, they were reported in the same order as the source data.

                  Changes in version 1.14 (2017-07-10)                  

    o   Adjusted maximum multi-core allowance to 90% of available processor cores.

                  Changes in version 1.13 (2017-07-08)                  

    o   Submission to CRAN

    o   Minor vignette updates.

                        Changes in version 1.12                         

    o   Changes in version 1.10 and v1.11 restricted to internal releases.

    o   Transferred github repository location to github.com/IgDAWG/BIGDAWG

    o   Added multi-core capabilities to haplotype analysis to speed up pairwise analysis. Useful for large datasets.

    o   Update to haplotype output files.

    o   Analysis results can be merged into single files with Merge.Output=T. Not recommend for very large datasets and running all pairwise combinations in the haplotype analysis.

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.28.0, 2017-04-13)

                         Changes in version 1.9                         

    o   Added warning that when All.Pairwise=T or the locus or amino acid tests are run with multiple sets, there will be duplication of analyses and results when sets contain overlapping loci.

    o   When All.Pairwise=T, only pairwise combinations are run in the haplotype analysis.

    o   Changes to output list structure when Return=T.

    o   Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.27.0, 2017-01-20)

                        Changes in version 1.8.4                        

    o   Naming update to haplotype output files. Haplotype loci will no longer be appended to the filename. When All.Pairwise=T, the filename will be appended with "PairwiseSet" and the set number. A file will also be written to indicate which pairwise set corresponds to which haplotypes.

                        Changes in version 1.8.3                        

    o   Updated vignette

                        Changes in version 1.8.2                        

    o   Small adjustments to console output for clarity and grammar.

    o   Moved knitr and rmarkdown from Suggests to Imports.

                        Changes in version 1.8.1                        

    o   Adjustment to data output merging function.

    o   Small fix to 'A' analysis when output to object.

                         Changes in version 1.8                         

    o   Added output of merged analyses to main output folder (only when Output = T).

                         Changes in version 1.7                         

    o   Adjusted function for counting missing alleles to avoid memory limitations. Ported from haplo.stats.

                         Changes in version 1.6                         

    o   Update bundled IMGT/HLA amino acid exon alignment to latest release (3.26.0.1)

    o   Update to URL for downloading *_prot.txt alignment files

    o   Small fixes to UpdateRelease code when downloading alignment files from IMGT.

                        Changes in version 1.5.8                        

    o   Fix bug that may be encountered when specifying a set of loci to run.

                        Changes in version 1.5.7                        

    o   Pandoc requirement for installing from GitHub without RStudio. Thanks to Hugh Salamon.

                        Changes in version 1.5.6                        

    o   URL change for 'hla_nom_p.txt' download. Thanks to Hugh Salamon.

                 Changes in version 1.5.5 (2016-08-31)                  

    o   Bug fixed - accidently introduced in v1.5.4 that would cause 'A' test failure

                 Changes in version 1.5.4 (2016-08-28)                  

    o   Small changes in code organization.

    o   Update bundled IMGT/HLA amino acid exon alignment to latest release (3.25.0)

                        Changes in version 1.5.3                        

    o   Fix bug in UpdateRelease() on some installations.

                        Changes in version 1.5.2                        

    o   Fix for an incorrect error message wording. Thanks to Farrel Buchinsky.

    o   Fix for data read-in when 1-Field resolution. Thanks to Farrel Buchinsky.

                        Changes in version 1.5.1                        

    o   Bug fix in output list.

                        Changes in version 1.5.0                        

    o   BIGDAWG can now return results as list with parameter Return=T.

    o   Minimize console output with Verbose=F.

    o   Turn off write results to file with Output=F.

    o   Bug fix for DRB3/4/5 parsing with NA's.

                 Changes in version 1.4.0 (2016-05-14)                  

    o   Version change, submission to CRAN.

                        Changes in version 1.3.9                        

    o   Vignette link modifications.

    o   Bug fix for UpdateRelease() when there is no internet connection.

                        Changes in version 1.3.8                        

    o   Error message for allele formatting imbalance across loci when HLA=T.

                        Changes in version 1.3.7                        

    o   Bug fix for CheckRelease() when there is no internet connection.

    o   Bug fix when setting Output=F, for testing only.

    o   Bug fix HWE displaying control analysis twice.

    o   Minor changes to vignette.

    o   Adjust Errors to only print out when Output=T.

                        Changes in version 1.3.6                        

    o   Added function to check Changes in version ersion and IMGT/HLA version simultaneously using CheckRelease().

    o   Removed UpdateRelease(GetRelease). See vignette.

    o   Vignette update to reflect changes.

                        Changes in version 1.3.5                        

    o   Minor wording change to vignette to enhance clarity and reflect GitHub availability.

    o   Added function to check release BIGDAWG uses for IMGT/HLA database. See vignette.

    o   Added Hardy Weinberg Equilibrium testing for cases. Useful when employing other binary phenotypes.

    o   Update bundled IMGT/HLA amino acid exon alignment to latest release (3.24.0)

                 Changes in version 1.3.4 (2016-04-10)                  

    o   Added output of subject haplotypes to file when running haplotype analysis.

    o   Bug fix in haplotype generation and outputs.

    o   Bug fix in when locus has only a single allele. Thanks go to Antoine Lizee.

    o   Other minor improvements to enhance data processing.

    o   Minor wording change to vignette to enhance clarity.

    o   Updated Human Immunology paper to BIGDAWG.

    o   Added ability to read in HLA data when DRB3, DRB4, and DRB5 are collapsed to a single column. DR haplotypes are parsed accordingly. See vignette for details.

    o   Added output of Sample IDs removed due to missing alleles exceeding set threshold.

    o   Adjusted Missing default to 2.

    o   When running multiple locus sets the for haplotype analysis, now displays which haplotype is being run.

                 Changes in version 1.2.8 (2016-02-29)                  

    o   Bug fix.

                        Changes in version 1.2.7                        

    o   Bug fix for chi square output using some data sets.

                 Changes in version 1.2.6 (2016-02-20)                  

    o   BIDAWG v1.2.1 - v1.2.5 unreleased internal versions.

    o   Bug fix when removing missing data as set by 'Missing' parameter. Thanks go to Arun Khattri.

    o   Added reference to BIGDAWG publication in DESCRIPTION and vignette.

    o   Update bundled IMGT/HLA amino acid exon alignment to latest release (3.23.0)

                 Changes in version 1.2.1 (2015-11-10)                  

    o   Added NEWS file to document BIGDAWG releases.

    o   Bug fix when EVS.rm was set to TRUE.

    o   Precheck.txt renamed to Data_Summary.txt.

    o   Distinction between Run parameters and Set parameters.

    o   Run Parameters generated and written to file earlier in script.

    o   Added section delimiter for 'Data Processing And Checks' in console output.

    o   Changes in wording for select BIGDAWG error messages.

    o   Update to Hardy-Weinberg test.

    o   Update bundled IMGT/HLA amino acid exon alignment to latest release (3.22.0)
