Add information in README.md on how to cite the package

Author: hpages

R/cache-utils.R

@@ -42,7 +42,7 @@ igblastr_cache <- function(which=NULL)
         GERMLINE_DBS    =file.path(path, "germline_dbs"),
         C_REGION_DBS    =file.path(path, "c_region_dbs"),
         IMGT_LOCAL_STORE=file.path(path, "store", "IMGT-releases"),
-	stop(wmsg("'which' must be one of ",
+        stop(wmsg("'which' must be one of ",
                   paste0("\"", .IGBLASTR_CACHES, "\"", collapse=", ")))
     )
 }

R/igblast_info.R

@@ -75,7 +75,7 @@ normalize_igblast_organism <- function(organism)
                            silent=TRUE)
         if (!system_command_worked(raw_version))
             stop(wmsg("command '", cmdpath, " -version' failed"))
-	.IGBLAST_VERSION_cache[[cmdpath]] <- raw_version
+        .IGBLAST_VERSION_cache[[cmdpath]] <- raw_version
     }
     if (raw.version)
         return(raw_version)

README.md

@@ -5,6 +5,26 @@
 
 **igblastr** is an R/Bioconductor package that provides functions to conveniently install and use a local IgBLAST installation from within R.
 
+To cite the **igblastr** package in publications, please use:
+
+Pagès H, Hyrien O, MacPhee K, Duff M, Taylor J (2025).
+_igblastr: User-friendly R Wrapper to IgBLAST_.
+doi:10.18129/B9.bioc.igblastr
+<https://doi.org/10.18129/B9.bioc.igblastr>.
+<https://bioconductor.org/packages/igblastr>.
+
+A BibTeX entry for LaTeX users is
+```
+@Manual{,
+  title = {igblastr: User-friendly R Wrapper to IgBLAST},
+  author = {Hervé Pagès and Ollivier Hyrien and Kellie MacPhee and Michael Duff and Jason Taylor},
+  year = {2025},
+  doi = {10.18129/B9.bioc.igblastr},
+  url = {https://bioconductor.org/packages/igblastr},
+}
+```
+Please also cite the original IgBLAST tool if you use it in your analysis.
+
 See <https://bioconductor.org/packages/igblastr> for more information,
 including for how to install the release version of the package (please refrain
 from installing directly from GitHub).

tests/testthat/test-precompiled-igblast-utils.R

@@ -2,7 +2,7 @@ test_that("inst/extdata/ncbi_igblast_data_files/ is not out-of-sync", {
     ## igblastr:::check_ncbi_igblast_data_files() is not guaranteed to work
     ## on Windows.
     if (.Platform$OS.type != "windows") {
-	prev_warn <- getOption("warn")
+        prev_warn <- getOption("warn")
         options(warn=2)
         on.exit(options(warn=prev_warn))
         igblastr:::check_ncbi_igblast_data_files(get_igblast_root())