NEWS

---

gwas2crispr 0.1.5 (2026-06-02)

• Expanded trait identifier validation: Expanded accepted GWAS Catalog trait identifier formats beyond the original EFO-only validation.
• Backward compatibility preserved: Preserved the existing efo_id argument and --efo CLI option for backward compatibility.
• Identifier normalization added: Added identifier normalization for underscore and colon formats.
• Selected supported prefixes: Added support for selected disease and cancer trait identifier prefixes including EFO, MONDO, and NCIT when supported by the GWAS Catalog API.
• Compatibility prefixes accepted: Added compatibility validation for selected phenotype and rare-disease prefixes, including HP, Orphanet, and ORPHA.
• GO explicitly rejected: Explicitly rejected GO identifiers as primary GWAS Catalog trait identifiers in gwas2crispr 0.1.5.
• Retrieval cascade improved: Added direct identifier-based association retrieval attempts before label-based retrieval.
• Coordinate recovery improved: Improved coordinate recovery for rsID records when GWAS Catalog responses lack complete GRCh38 coordinates.
• Optional Ensembl fallback added: Added optional non-fatal Ensembl REST fallback for missing rsID coordinates.
• CLI, documentation, and tests updated: Updated CLI validation, documentation, and tests.

gwas2crispr 0.1.4 (2026-05-09)

• GWAS Catalog REST API v2 backend: Replaced the former third-party GWAS retrieval workflow with direct EMBL-EBI GWAS Catalog REST API v2 retrieval.
• Removed old GWAS retrieval dependency: Removed gwasrapidd from package dependency metadata, code, tests, and user-facing documentation.
• Updated fetch_gwas() output: fetch_gwas() now returns a package-native list with:
  • associations
  • risk_alleles
  • cache
• Updated run_gwas2crispr() integration: run_gwas2crispr() now consumes the new package-native fetch_gwas() result and no longer expects an S4 associations object.
• Direct endpoint workflow: Added direct handling for GWAS Catalog REST API v2 trait resolution, association retrieval, and SNP metadata retrieval.
• Optional FASTA behavior improved: CSV and BED outputs remain available even when FASTA dependencies are unavailable. FASTA is generated only when BSgenome.Hsapiens.UCSC.hg38 and Biostrings are installed.
• Output path handling improved: run_gwas2crispr() no longer returns NA entries inside the written vector when FASTA output is skipped.
• Summary logic improved: SNPs_w_gene is now calculated as the number of distinct SNPs with gene annotation, avoiding inflated counts when variants appear in multiple association rows.
• Tests updated: Updated tests for input validation, direct REST API output structure, optional FASTA behavior, safe writing to tempdir(), and no-default-write behavior.
• Documentation updated: Updated README, cran-comments.md, roxygen documentation, and package metadata for the direct GWAS Catalog REST API v2 workflow.
• Version bump: Bumped package version to 0.1.4.

gwas2crispr 0.1.2 (2025-08-22)

• CLI improvements: The command-line script (inst/scripts/gwas2crispr.R) no longer forces file output. The --out/-o option is now truly optional: omit it to run the pipeline in memory without writing any files. A new --verbose/-v flag prints a concise summary when no outputs are written. The double comma in the option definition has been fixed.
• Console output: All side-effects (print()/cat()) have been replaced with message() behind a verbose flag. By default, functions run quietly unless verbose = TRUE or the new CLI flag is used.
• Testing: Added tests/testthat/test-run_gwas2crispr.R to ensure that run_gwas2crispr() writes only to a provided out_prefix and returns objects without writing by default.
• Documentation: Updated DESCRIPTION with expanded acronyms and method references; ensured Language: en-US and valid Bioconductor biocViews. Updated the README and vignette to reflect the new no-default-write behaviour and optional CLI output. Added a simple inst/CITATION entry. Bumped version to 0.1.2.

gwas2crispr 0.1.1

• Addressed CRAN review comments:
  • Expanded acronyms in DESCRIPTION: GWAS, EFO, SNP, BED, FASTA, and CRISPR.
  • Added method reference: Sudlow et al. (2015) doi:10.1093/nar/gkv1256.
  • Replaced \dontrun{} with \donttest{} where network I/O may occur.
  • Kept examples short.
  • Ensured run_gwas2crispr(out_prefix = NULL) returns objects only and does not write files by default.
  • Ensured examples, vignette, and tests write only to tempdir() when file output is needed.
  • Made console output suppressible via verbose and message().
• Qualified utils::capture.output to avoid NOTES.
• Updated vignette with object-only example by default and optional tempdir() example for file outputs.
• Fixed CLI script by correcting the --out option to use type = "character".
• Fixed CITATION by defining the meta object before using meta$Version.
• Corrected the Language field.
• Expanded DESCRIPTION with acronym explanations and references.

gwas2crispr 0.1.0

• Initial public release.
• Fetch GWAS associations and export CSV, BED, and FASTA outputs for GRCh38/hg38.
• Added CLI script at inst/scripts/gwas2crispr.R.