WangLabCSU · Yunuuuu · Sep 19, 2025 · May 28, 2025 · Jun 3, 2025 · Jun 4, 2025
diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,7 @@
 .Rproj.user
+.Rhistory
 .radian_history
 Scratch.RConsole
-
 /.quarto/
 README.html
 docs
diff --git a/NAMESPACE b/NAMESPACE
@@ -8,6 +8,7 @@ export(appmamba_rc)
 export(arg)
 export(arg0)
 export(bcftools)
+export(bedtools)
 export(bowtie2)
 export(cellranger)
 export(cmd_background)

diff --git a/R/cmd-bedtools.R b/R/cmd-bedtools.R
@@ -0,0 +1,38 @@
+#' Run bedtools
+#'
+#' The `bedtools` is a powerful toolset for genome arithmetic.
+#' @param subcmd Sub-Command of bedtools. Details see: `r rd_help("bedtools")`.
+#' @param ... `r rd_dots("bedtools")`.
+#' @param bedtools `r rd_cmd("bedtools")`.
+#' @seealso
+#' - <http://bedtools.readthedocs.io/>
+#' - <https://github.com/arq5x/bedtools2/>
+#'
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
+#' @export
+bedtools <- make_command(
+  "bedtools",
+  function(subcmd = NULL, ..., bedtools = NULL) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(bedtools, allow_empty = FALSE, allow_null = TRUE)
+    BEDTools$new(cmd = bedtools, ..., subcmd = subcmd)
+  }
+)
+
+BEDTools <- R6Class(
+  "BEDTools",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools",
+    setup_help_params = function() "--help",
+    combine_params = function(subcmd) {
+      if (private$help) {
+        c(super$combine_params(), subcmd)
+      } else {
+        c(subcmd, super$combine_params())
+      }
+    }
+  )
+)
diff --git a/man/allele_counter.Rd b/man/allele_counter.Rd
diff --git a/man/bcftools.Rd b/man/bcftools.Rd
diff --git a/man/bedtools.Rd b/man/bedtools.Rd
diff --git a/man/blit-package.Rd b/man/blit-package.Rd
diff --git a/man/bowtie2.Rd b/man/bowtie2.Rd
diff --git a/man/cellranger.Rd b/man/cellranger.Rd
diff --git a/man/conda.Rd b/man/conda.Rd
diff --git a/man/exec.Rd b/man/exec.Rd
diff --git a/man/fastp.Rd b/man/fastp.Rd
diff --git a/man/fastq_pair.Rd b/man/fastq_pair.Rd
diff --git a/man/gistic2.Rd b/man/gistic2.Rd
diff --git a/man/kraken2.Rd b/man/kraken2.Rd
diff --git a/man/kraken_tools.Rd b/man/kraken_tools.Rd
diff --git a/man/perl.Rd b/man/perl.Rd
diff --git a/man/pyscenic.Rd b/man/pyscenic.Rd
diff --git a/man/python.Rd b/man/python.Rd
diff --git a/man/samtools.Rd b/man/samtools.Rd
diff --git a/man/seqkit.Rd b/man/seqkit.Rd
diff --git a/man/snpEff.Rd b/man/snpEff.Rd
diff --git a/man/trust4.Rd b/man/trust4.Rd
diff --git a/man/varscan.Rd b/man/varscan.Rd
diff --git a/tests/testthat/test-exec.R b/tests/testthat/test-exec.R
@@ -3,6 +3,11 @@ testthat::test_that("`allele_counter()` works as expected", {
     allele_counter() |> cmd_help()
 })
 
+testthat::test_that("`bedtools()` works as expected", {
+    testthat::skip_if_not(nzchar(Sys.which("bedtools")))
+    bedtools() |> cmd_help()
+})
+
 testthat::test_that("`cellranger()` works as expected", {
     testthat::skip_if_not(nzchar(Sys.which("cellranger")))
     cellranger() |> cmd_help()