BIGDAWG v1.12 (Release date: 2017-06-21) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* BIGDAWG v1.10 & v1.11 restricted to internal releases.
* Transferred github repository location to github.com/IgDAWG/BIGDAWG
* Added multi-core capabilities to haplotype analysis to speed up pairwise analysis. Useful for large datasets.
* Update to haplotype output files.
* 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.
* Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.28.0, 2017-04-13)

BIGDAWG v1.9 (Release date: 2017-01-20) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* 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.
* When All.Pairwise=T, only pairwise combinations are run in the haplotype analysis.
* Changes to output list structure when Return=T.
* Updated bundled IMGT/HLA amino acid exon alignment to latest release (Release 3.27.0, 2017-01-20)

BIGDAWG v1.8.4 (Release date: 2017-01-12) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* 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.

BIGDAWG v1.8.3 (Release date: 2016-12-26) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Updated vignette

BIGDAWG v1.8.2 (Release date: 2016-12-14) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Small adjustments to console output for clarity and grammar.
* Moved knitr and rmarkdown from Suggests to Imports.

BIGDAWG v1.8.1 (Release date: 2016-12-13) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Adjustment to data output merging function.
* Small fix to 'A' analysis when output to object.

BIGDAWG v1.8 (Release date: 2016-12-10) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Added output of merged analyses to main output folder (only when Output = T).

BIGDAWG v1.7 (Release date: 2016-12-08) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Adjusted function for counting missing alleles to avoid memory limitations. Ported from haplo.stats.

BIGDAWG v1.6 (Release date: 2016-12-02) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Update bundled IMGT/HLA amino acid exon alignment to latest release (3.26.0.1)
* Update to URL for downloading *_prot.txt alignment files
* Small fixes to UpdateRelease code when downloading alignment files from IMGT.

BIGDAWG v1.5.8 (Release date: 2016-12-02) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Fix bug that may be encountered when specifying a set of loci to run.

BIGDAWG v1.5.7 (Release date: 2016-10-05) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Pandoc requirement for installing from GitHub without RStudio. Thanks to Hugh Salamon.

BIGDAWG v1.5.6 (Release date: 2016-09-14) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* URL change for 'hla_nom_p.txt' download. Thanks to Hugh Salamon.

BIGDAWG v1.5.5 (Release date: 2016-08-29) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Bug fixed - accidently introduced in v1.5.4 that would cause 'A' test failure

BIGDAWG v1.5.4 (Release date: 2016-08-26) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Small changes in code organization.
* Update bundled IMGT/HLA amino acid exon alignment to latest release (3.25.0)

BIGDAWG v1.5.3 (Release date: 2016-08-25) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Fix bug in UpdateRelease() on some installations.

BIGDAWG v1.5.2 (Release date: 2016-08-03) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Fix for an incorrect error message wording. Thanks to Farrel Buchinsky.
* Fix for data read-in when 1-Field resolution. Thanks to Farrel Buchinsky.

BIGDAWG v1.5.1 (Release date: 2016-06-20) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Bug fix in output list.

BIGDAWG v1.5.0 (Release date: 2016-06-15) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* BIGDAWG can now return results as list with parameter Return=T.
* Minimize console output with Verbose=F.
* Turn off write results to file with Output=F.
* Bug fix for DRB3/4/5 parsing with NA's.

BIGDAWG v1.4.0 (Release date: 2016-05-12) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Version change, submission to CRAN.

BIGDAWG v1.3.9 (Release date: 2016-05-11) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Vignette link modifications.
* Bug fix for UpdateRelease() when there is no internet connection.

BIGDAWG v1.3.8 (Release date: 2016-05-04) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Error message for allele formatting imbalance across loci when HLA=T.

BIGDAWG v1.3.7 (Release date: 2016-04-29) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Bug fix for CheckRelease() when there is no internet connection.
* Bug fix when setting Output=F, for testing only.
* Bug fix HWE displaying control analysis twice.
* Minor changes to vignette.
* Adjust Errors to only print out when Output=T.

BIGDAWG v1.3.6 (Release date: 2016-04-26) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Added function to check BIGDAWG version and IMGT/HLA version simultaneously using CheckRelease().
* Removed UpdateRelease(GetRelease). See vignette.
* Vignette update to reflect changes.

BIGDAWG v1.3.5 (Release date: 2016-04-20) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Minor wording change to vignette to enhance clarity and reflect GitHub availability.
* Added function to check release BIGDAWG uses for IMGT/HLA database. See vignette.
* Added Hardy Weinberg Equilibrium testing for cases. Useful when employing other binary phenotypes.
* Update bundled IMGT/HLA amino acid exon alignment to latest release (3.24.0)

BIGDAWG v1.3.4 (Release date: 2016-04-08) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Added output of subject haplotypes to file when running haplotype analysis.
* Bug fix in haplotype generation and outputs.
* Bug fix in when locus has only a single allele. Thanks go to Antoine Lizee.
* Other minor improvements to enhance data processing.
* Minor wording change to vignette to enhance clarity.
* Updated Human Immunology paper to BIGDAWG.

BIGDAWG v1.3.1 - v1.3.3 (Internal Releases) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* 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.
* Added output of Sample IDs removed due to missing alleles exceeding set threshold.
* Adjusted Missing default to 2.
* When running multiple locus sets the for haplotype analysis, now displays which 
  haplotype is being run.

BIGDAWG v1.2.8 (Release date: 2016-02-28) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Bug fix.

BIGDAWG v1.2.7 (Release date: 2016-02-27) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Bug fix for chi square output using some data sets.

BIGDAWG v1.2.6 (Release date: 2016-02-19) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* BIDAWG v1.2.1 - v1.2.5 unreleased internal versions.
* Bug fix when removing missing data as set by 'Missing' parameter. Thanks go to Arun Khattri.
* Added reference to BIGDAWG publication in DESCRIPTION and vignette.
* Update bundled IMGT/HLA amino acid exon alignment to latest release (3.23.0)

BIGDAWG v1.2.1 (Release date: 2015-11-09) Derek Pappas <dpappas@chori.org>
====================================================================================
Changes:
* Added NEWS file to document BIGDAWG releases.
* Bug fix when EVS.rm was set to TRUE.
* Precheck.txt renamed to Data_Summary.txt.
* Distinction between Run parameters and Set parameters.
* Run Parameters generated and written to file earlier in script.
* Added section delimiter for 'Data Processing And Checks' in console output.
* Changes in wording for select BIGDAWG error messages.
* Update to Hardy-Weinberg test.
* Update bundled IMGT/HLA amino acid exon alignment to latest release (3.22.0)
