### HLAtools

### version 1.6.3
- July 20, 2025
- Changed all instances of 'HLAgazeteer' in the package to 'HLAgazetteer'. The former 'HLAgazeteer' object is now the 'HLAgazetteer', and the former 'buildGazeteer()' function is now 'buildGazetteer()'.
- Removed the 'HLAgazeteer' object from the package and added the 'HLAgazetteer' object, for version 3.61.0.
- Updated the fragmentFeatureNames and HLAatlas objects to version 3.61.0.
- Silenced warnings from atlasMaker() and buildAlignments() that occur when the the length of allele sequences in the 'appendix' of an alignment are unequal.

### version 1.6.2
- May 1, 2025
- Changed |> to %>% operator in buildIMGTHLAGeneTypes() to maintain compatibility with R version 3. Package is now compatible with R version 3.6.0 and later.

### version 1.6.1
- April 30, 2025
- Added the 'acc' parameter to verifyAllelle(), appending the IPD-IMGT/HLA accession number for a specified allele to the returned object.
- Updated News and Vignette.
- Submission to CRAN.

### version 1.6.0
- April 29, 2025
- Added the queryPositions() and variantTable() functions, identifying variants at specified positions in any alignment in HLAalignments.
- Updated News and Vignette.

### version 1.5.0
- April 20, 2025
- Refactored the buildIMGTHLAGeneTypes() function to accommodate the transition of the "molecular characteristics data for HLA region genes" web-page from 'hla.alleles.org/genes/index.html' to 'hla.alleles.org/pages/genes/genes_list'.
- Updated updateAll() to account for the transition from 'hla.alleles.org/genes/index.html' to 'hla.alleles.org/pages/genes/genes_list' for updating IMGTHLAGeneTypes.
- Added the validatePositions() function to determine if specified positions exist in a specified type of alignment. 
- Applied validatePosition() for customAlign(), and updated the customAlign() documentation.
- Updated buildGazeteer() to include the DRB8 gene in HLAgazeteer$align.
- Updated IMGTHLAGeneTypes, HLAgazeteer and HLAtlas to version 3.60.0.
- Added the rvest and stats packages to Imports.
- The alleleListHistory dataset for IPD-IMGT/HLA Database release versions 3.60.0 and later is too large to be included in the package. The updateAll() function can be applied to load the alleleListHistory object for releases after 3.59.0.

### Version 1.4.0

- March 1, 2025
- Updated verifyAllele() to identify all releases in which an allele name appears or the first (oldest) release in which that name appeared. 
- Updated getField() to eliminate duplication of expression variant suffixes, and exit gracefully when 'append' is not a logical value. 
- Added the translateAllele(), translateGLstring(), multiTranslateGLstring() functions. 
- Refactored updateGL(), GLupdate() and multiUpdateGL() for efficiency, and to ensure translation across all IPD-IMGT/HLA Release Versions. Replaced the 'GLstring' parameter in these functions with the 'GLSC' parameter.
- Added the verbose parameter to updateGL(), GLupdate() and multiUpdateGL().
- Updated validateGLstring() and translateAllele() to account for the "w" in "Cw.
- Updated GIANT() to interchange the "C" and "Cw" locus names when HLA-C data are translated across nomnenclature epoch 1 or 2 allele names and epoch 3 allele names.
- Updated GIANT(), updateGL() and multiUpdateGL() to use checkVersion() rather than validateVersion().
- Updated the description of the vector returned by countSpaces().
- Added examples for customAlign() and alignmentSearch().
- Corrected formatting, spelling and grammatical errors in the documentation of several functions.  
- NOTE: GLupdate() is maintained in this release for compatibility with previous releases, but will be removed in a future release.
- Updated News and Vignette.

### Version 1.3.0

- November 11, 2024
- HLAatlas, HLAgazeteer, alleleListHistory and fragmentFeatureNames updated to IPD-IMGT/HLA Database release 3.58.0.
- Exported HLAgazeteer for use in validateLocus(), multiLocusValidation(), and buildAlignments().
- Updated buildAlignments() to append expression suffixes to the truncated names of 3- and 4-field alleles with expression variant suffixes.
- Added multiQueryRelase(), extending queryRelease() to search for multiple allele-name elements.
- Updated the package vignette.
- Spelling corrections in fragmentFeatureNames documentation.

### Version 1.2.0

- August 20, 2024
- Added multiAlleleTrim() for trimming vectors of allele names in a single nomenclature epoch.

### Version 1.1.4

- August 16, 2024
- Revised multiUpdateGL() to avoid collisions between allele names and version identifiers, improve messaging and efficiency, update sets of GL String Codes generated under different release versions, and append "HLA-" to allele names in returned GLSCs.
- Changed release version in GLSC.ex dataset from 3.1.0 to 3.01.0.
- Updated alleleTrim() to optionally include expression variants in truncated allele names.

### Version 1.1.3

- August 2, 2024
- Package version 1.1.1 published on CRAN Repository on July 26, 2024.
- Updated the feature names for HLA-R in fragmentFeatureNames. 
- Described all four non-standardard features in ffN() documentation.
- Minor corrections to vignette.
- Updated package Description.

### Version 1.1.2

- July 24 to July 25, 2024
- Updated the bundled HLAatlas object to include non-standard features for the HLA-R gDNA atlas.
- Changed the date on the IMGTHLAGeneTypes object from "09-07-2024" to "08-07-2024" to reflect the date on the updated hla.alleles.org/genes/index.html page.
- Corrected a typo in documentation for ffn().
- Updated atlasMaker() to return non-standard gene feature names for the HLA-R, -S, -T, -V, and -W cDNA atlases.
- Noted non-standard features in HLAatlas and atlasMaker documentation.
- Updated data/HLAatlas.rda file to reflect these changes.

### Version 1.1.1

- July 21, 2024
- Added link to ANHIG/IMGTHLA GitHub repo in Description.
- Removed example from BuildIMGTHLAGeneTypes().
- Modified updateAll() to load new objects into the parent.frame() environment, rather than .GlobalEnv.
- Submission to CRAN. 

### Version 1.1.0

- July 17, 2024
- Added the GIANT() function for translating vectors and data frames of HLA allele names across IPD-IMGT/HLA Database release versions.
- Updates to ReadMe and Vignette.
- Updates to function examples.
- Submission to CRAN.

### Version 1.0.4

- July 12, 2024
- Modified functions to support and incorporate the new HLA-R gene.
- Corrected fragmentFeaturesNames annotations for HLA-P and -W.
- Updated the alleleListHistory, fragmentFeatureNames, HLAgazeteer and HLAatlas data objects to version 3.57.0, and IMGTHLAGeneTypes to version 09-07-2024, and aded these versions to the package.

### Version 1.0.3

- July 10, 2024
- Corrected typo in queryRelease() documentation.
- Expanded acronyms in DESCRIPTION.
- Added 'value' lines to addCodonLine(), getField(), typeToSource() and updateAll().
- Minor edits to other function descriptions.
- Replaced 'dontrun' with 'donttest' in function documentations, or remove 'dontrun' in some cases.
- Removed note for atlasFull().
- Removed pseudo.codon global variable and zzz.R file.
- Updated GLVhelper() for full release versions 1.*, 2.* and 3.* functionality. 
- Streamlined updateGL() functionality and include informative examples.
- Updated documentation and examples for GLupdate(),  GLV(), GLV2, redec(). 
- Updated GLVhelper() functoinality, documention and messaging.
- Added 'namespace' parameter to GLvalidate(), supporting HLA and KIR GLSC namespaces, although KIR is not supported in the HLAtools package.
- Added BIGDAWG-formatted sHLAdata synthetic dataset for use with BDstrat(), BDtoPyPop() and relRisk().
- Added calls to sHLAdata in  BDstrat(), BDtoPyPop() and relRisk() examples.
- Updated ReadMe and Vignette.

### Version 1.0.2

- June 28, 2024
- Removed GPL license document.
- Adopted canonical URL to BIGDAWG input format in relRisk() and BDStrat().
- Added URL to HLAtools GitHub repository.
- Correct titles for ExpandVersion() and GLtoUN() functions.
- Submission to CRAN.

### Version 1.0.1

- June 27, 2024
- Wrapped individual authors in c() in DESCRIPTION.
- Limited 'cre' role to the package Maintainer.
- Submission to CRAN.

### Version 1.0.0

- June 26, 2024
- Standardized function documentation.
- Remove write.table() calls from atlasMaker().
- Add save.path parameter to BDtoPyPop() and relRisk().
- initial package release.
- Submission to CRAN.

### Version 0.9.16.9000 June 24th to 25th, 2024

- Updated atlasMaker() to build atlases for DRB1 in release 3.48.0.
- Updated atlasMaker() to build atlases for HLA-B in releases 3.44.0 and 3.43.0.
- Updated atlasMaker() to build atlases for HFE in releases 3.27.0 to 3.22.0. 
- Updated atlasMaker() to build atlases for HLA-V in release 3.14.0.
- Updated atlasMaker() to build atlases for DPA2 and DPB2 in releases 3.53.0-3.27.0.
- Updated atlasMaker() to build atlases for HLA-N, -S, -U, and -Y in releases 3.35.0-3.33.0.
- Updated atlasMaker() to build atlases for HLA-Y in releases 3.32.0-3.20.0.
- Updated atlasMaker() to build atlases for HLA-W and -T in release 3.27.0.
- Updated atlasMaker() to build atlases for All loci in release 3.13.0/3.13.1.
- Updated atlasMaker() to build atlases for HLA-C in release 3.02.0.
- Updated atlasMaker() to build atlases for DPA, DPB, TAP1 and TAP2 in release 3.00.0.
- Stopped atlasMaker() writing correspondence_tables to tempdir.

### Version 0.9.15.9000 June 21, 2024

- Added addCodonLine() function to facilitate fixing nucleotide alignments that are missing "AA codon" lines.

### Version 0.9.14.9000 June 10th to 20th, 2024

- Updated buildAlignments() to build DPA2 and DPB2 cDNA alignments in releases prior to 3.54.0.
- Updated buildAlignments() to build DRB1 gDNA alignments in release 3.48.0.
- Updated buildAlignments() to build HLA-B cDNA alignments in releases 3.44.0 and 3.43.0.
- Updated buildAlignments() to build HLA-N, -S, -U and -Y cDNA alignments in releases prior to 3.36.0.
- Updated buildAlignments() to build HLA-W and -T cDNA alignments in release 3.27.0.
- Updated buildAlignments() to build HFE cDNA alignments in releases prior to 3.28.0.
- Updated buildAlignments() to build HLA-DPA, -DPB, -DQA and -DQB AA alignments in releases prior to 3.24.0. The returned objects are "$DPA", "$DPB", "$DQA" and "$DQB", the loci in these objects are "DPA1", "DPB1", "DQA1" and "DQB1".
- Updated buildAlignments() to build HLA-V in version 3.14.0.
- Updated buildAlignments() to account for version inconsistency (3.13.0 vs 3.13.1) in release 3.13.1 alignments.
- Updated documentation of repoVersion() for accuracy.
- Applied repoVersion() in buildAlignments().
- Modified buildGazeteer() to account for version differences in URL and alignment files for release 3.13.0/3.13.1.
- Updated buildAlignments() to build HLA-C cDNA alignments in release 3.02.0.
- Close connections in HLAgazeteer().
- Updated buildAligmments() to build HLA-DOA AA alignment in release 3.01.0.
- Updated documentation for updateAll().
- Updated repoVersion() for release 3.00.0.
- Updated buildAlignments() to build HLA-DPA and -DPB cDA alignments in release 3.00.0.
- Updated buildAlignments() to build TAP1 and TAP2 cDNA alignments in version 3.00.0.

### Version 0.9.13.9000 June 4, 2024

- Clarified that the oldest available release for GL String Code updating is version 1.05.0.
- Changed the default IMGT/HLA Release version for alignmentFull() to the version of the loaded HLAgazeteer.

### Version 0.9.12.9000 May 28, 2024

- Added motifMatch() and validateMotif() functions. Thanks to Kazu Osoegawa for the suggestion.
- Updated documentation for checkAlignType().
- Corrected documentation for fragmentFeatureNames.

### Version 0.9.11.9000 May 16, 2024

- Updated package title.
- Minor updates to Vignette.
- Changed '*' to '#' for PyPop version references.
- Complete citations for published sources of the HLAgazeteer.
- Limited asterisks in function parameter documentation.
- Added link to PyPop configuration file webpage in pypopHeaders().
- Added locus sanity check in compareSequences().
- Modified getField() so that NA values are not appended to an allele name when a resolution higher than that of the provided allele is requested.

### Version 0.9.10.9000 May 10, 2024 

- Updated buildGazeteer() to account for the DRB2, DRB6, DRB7 and DRB9 gene.
- Updated documentation for HLAgazeteer regarding the DRB2, DRB6, DRB7 and DRB9 genes and the DRB alignment files. 
- Updated documentation for fragmentFeatureNames() regarding the DRB2, DRB6, DRB7 and DRB9 genes and genomic alignments.
- Updated the vignette to reflect these issues.

### Version 0.9.9.9000 May 3, 2024 

- Added BDtoPyPop() function.
- Updates to Vignette, ReadMe and Description.

### Version 0.9.8.9000 April 27, 2024

- Removed reliance on HTexceptions data object.
- Correction to relRisk().

### Version 0.9.7.9000 April 20, 2024

- Standardized use of 'source' in documentation. 
- Changed 'alignType' parameter to 'source' in multiLocusValidation().
- Added checkAlignType() and checkSource() functions for converting between alignmentType (for alignment objects) and source (for alignment files) values.
- Added checkAlignType() to AlignmentFull().
- Suppressed warning messages in alignmentFull() and atlasMaker().
- Restricted compareSequences() to a single 'alignType'.
- Clarified when only a single 'alignType' is allowed for a function.
- Edits to Vignette.

### Version 0.9.6.9000 April 15, 2024

- Added the queryRelease() function for searching the alleleListHistory object.
- Formalized and streamlined the GL String to UNIFORMAT and UNIFORMAT to GL String functions and updated documentation.
- Corrected documentation for customAlign().
- Corrected Markdown formatting in BDstrat.R.
- First draft of complete Vignette.

### Version 0.9.5.9000 April 11, 2024

- Added 'source' selection to multiLocusValidation().
- Modified atlasMaker() to support updated multiLocusValidation().
- Updated packaged data objects (HLAatlas,HLAgazeteer,fragmentFeatureNames and alleleListHistory) to version IPD-IMGT/HLA Database Release version 3.56.0.
- Updated Vignette.

### Version 0.9.4.9000 April 9, 2024

- Added HTexceptions() and the HTexceptions data object, which make defined exceptions for specific use cases available for package functions. 
- Added HTexceptions.rda to the /data folder. 
- Updated atlasMaker() to use HTexceptions for building DPA2, DPB2 and HLA-Y nucleotide atlases.
- Updated atlasMaker() to use multiLocusValidation(), which depends on the HLAgazeteer$version to evaluate locus:version matches. 
- Modified multiLocusValidation() messaging to reflect this dependence on HLAgazeteer$version.
- Updates to Vignette.
- Updates to ReadMe.

### Version 0.9.3.9000 April 7, 2024

- Correctly added GPL3 License to package.
- Added getAlignmentNames() function.
- Added repoVersion() function.
- Added parseAlignmentHead() function.
- Updated buildGazeteer() to use getAlignmentNames().
- Updated atlasMaker(), buildAlignments() and buildGazeteer() to use repoVersion().
- Updates to Vignette.
- Updates to ReadMe.

### Version 0.9.2.9000 April 3, 2024

- Added multiLocusValidation() function.
- Applied multiLocusValidation() in AlignmentFull().
- Closed connections in versionValidation().
- Added documentation to fragmentFeatureNames.R.
- Added content to Vignette.
- Corrected returned list names in BDstrat().
- Updated ReadMe.
- Updated documentation for relRisk().

### Version 0.9.1.9000 April 1, 2024

- Minor update to alignmentFull().
- Updated alignmentFull() documentation to note the absence of DP and DQ gene numbers in older database releases.
- Added sections to Vignette.
- Reformatted News to include bullets.

### Version 0.9.0.9000 March 31, 2024

- Updated BDStrat() to function on multiple alleles at multiple loci. 
- Added sections to Vignette.

### Version 0.8.1.9000 March 24, 2024

- Added the BDstrat() function for stratifying BIGDAWG-formatted datasets by single alleles 
- Added the verifyAllele() function, which leverages AlleleListHistory to determine if and when a full alllele name was valid.
- Updated ReadMe.

### Version 0.8.0.9000 March 21, 2024

- Added the relRisk() function for calculating relative risk using BIGDAWG-formatted datasets.
- Added $align to HLAgazeteer to identify all genes with alignments.
- Added new versions of the HLAatlas, HLAgazeteerm IMGTHLAGeneTypes, alleleListHistory, and fragmentFeatureNames objects to the package.
- Updated ReadMe.
- Added bullet points to News.

### Version 0.7.7.9000 March 19, 2024

- Updated posSort() and and alignmentSearch() to address edge-cases and support searching for intron positions.
- Updated getField() so that expression variant identifiers are optionally appended to truncated versions of full-length expression variants.
- Reestructured descriptions of several functions for clarity. 

### Version 0.7.6.9000 March 19, 2024

- Standardized versioning for the packaged data objects.  
- Added functionality for updating packaged data objects.  

### Version 0.7.5.9000 March 13, 2024

- Expanded HLAgazeteer to define multiple functional and organizational sets of genes.  
- Expanded alignmentFull() to build user-defined sets of alignments.   
- Updated ReadMe and Description to reflect expanded capacities.  

### Version 0.7.4.9000 February 18, 2024

- Consolidated sequence query and custom alignment building functions to support all alignments.  

### Version 0.7.3.9000 February 16, 2024

- Added a nucleotide ('nuc') aligmment to HLAalignments, and changed the previous 'nuc' alignment to 'codon'.  
- Nucleotide sequence query functions support both nucleotide and codon cDNA aligmnents.  

### Version 0.7.2.9000 February 10, 2024

- Added documentation, updated functions for building alignments.  
  
### Version 0.7.1.9000 February 9, 2024

- HLAtools Package contains reference datasets, along side query and analysis tools.  
