- Added OGRDB (AIRR Community) support with full suite of functions:
getOGRDB(): Download germline sets from OGRDBloadOGRDB(): Load OGRDB sequences into environmentrefreshOGRDB(): Update locally cached OGRDB sequenceslistOGRDB(): List archived OGRDB germline set versionsis_ogrdb_available(): Check OGRDB service availability
- Added export functions for popular immune repertoire analysis tools:
exportMiXCR(): Export sequences for MiXCR custom library buildingexportTRUST4(): Export sequences for TRUST4 analysisexportCellRanger(): Export sequences for 10x Cell Ranger VDJ referenceexportIgBLAST(): 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
- Added package-level man page (
immReferent-package) - Renamed getting-started vignette to
immReferentand 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
@seealsosections 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
- Set up GitHub Actions CI (R-CMD-check on macOS, Windows, Ubuntu)
- Added test coverage reporting via codecov
- Added PR command workflows for
/documentand/style - CI now runs on
main,master, anddevelbranches - Updated R version dependency from 4.2.0 to 4.5.0
- Added spelling wordlist
- Reorganized test suite: split monolithic test file into focused modules
test-mainIMGT.R,test-mainOGRDB.R,test-export.Rtest-cache.R,test-dowload.R,test-utils.R
- Added comprehensive unit tests for export, OGRDB, cache, download, and utility functions
- Fixed typo in
is_ogrdb_available()documentation (was incorrectly referencing IMGT) - Fixed BiocCheck findings from initial submission
- Initial release with IMGT sequence downloading, caching, and loading