NEWS

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immReferent 0.99.7

New Features

• Added OGRDB (AIRR Community) support with full suite of functions:
  • getOGRDB(): Download germline sets from OGRDB
  • loadOGRDB(): Load OGRDB sequences into environment
  • refreshOGRDB(): Update locally cached OGRDB sequences
  • listOGRDB(): List archived OGRDB germline set versions
  • is_ogrdb_available(): Check OGRDB service availability
• Added export functions for popular immune repertoire analysis tools:
  • exportMiXCR(): Export sequences for MiXCR custom library building
  • exportTRUST4(): Export sequences for TRUST4 analysis
  • exportCellRanger(): Export sequences for 10x Cell Ranger VDJ reference
  • exportIgBLAST(): Export sequences for IgBLAST database creation
• Export functions work with sequences from both IMGT and OGRDB sources
• Redirected HLA-based queries to IPD-IMGT/HLA FTP site for improved reliability
• Added support for additional species: cynomolgus monkey, pig, and dog

Documentation Improvements

• Added package-level man page (immReferent-package)
• Renamed getting-started vignette to immReferent and expanded content
• Expanded caching vignette with additional guidance
• Standardized roxygen2 documentation across all functions with proper formatting using \code{}, \strong{}, \itemize{}, and \url{}
• Added comprehensive @seealso sections linking related functions
• Improved parameter documentation with explicit type specifications
• Added return value documentation to OGRDB functions
• Added Bioconductor installation instructions to README and vignette

Infrastructure

• Set up GitHub Actions CI (R-CMD-check on macOS, Windows, Ubuntu)
• Added test coverage reporting via codecov
• Added PR command workflows for /document and /style
• CI now runs on main, master, and devel branches
• Updated R version dependency from 4.2.0 to 4.5.0
• Added spelling wordlist

Testing

• Reorganized test suite: split monolithic test file into focused modules
  • test-mainIMGT.R, test-mainOGRDB.R, test-export.R
  • test-cache.R, test-dowload.R, test-utils.R
• Added comprehensive unit tests for export, OGRDB, cache, download, and utility functions

Bug Fixes

• Fixed typo in is_ogrdb_available() documentation (was incorrectly referencing IMGT)
• Fixed BiocCheck findings from initial submission

immReferent 0.99.0

• Initial release with IMGT sequence downloading, caching, and loading