From 21150aea31d8442872d4c727ffc27c951652a949 Mon Sep 17 00:00:00 2001
From: wbq <2982433346@qq.com>
Date: Wed, 28 May 2025 11:24:50 +0800
Subject: [PATCH 01/10] add bedtools

---
 R/cmd-bedtools.R | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 R/cmd-bedtools.R

diff --git a/R/cmd-bedtools.R b/R/cmd-bedtools.R
new file mode 100644
index 0000000..e27a7bb
--- /dev/null
+++ b/R/cmd-bedtools.R
@@ -0,0 +1,39 @@
+#' Run bedtools
+#'
+#' The "bedtools" is a powerful toolset for genome arithmetic
+#' @param
+#' @param ... 'r rd_dots("bedtools")'.
+#' @param
+#' @param bedtools 'r rd_cmd("bedtools")'.
+#' @family command
+#' @inherit exec return
+#' @seealso
+#' - <https://github.com/arq5x/bedtools2/>
+#'
+#' 'r rd_seealso()'
+#' @export
+bedtools <- make_command(
+  "bedtools",
+  function(
+
+  ){
+    assert_string(bedtools,allow_empty = FALSE, allow_null = TRUE)
+    BEDTools$new(
+      cmd = bedtools,
+    )
+  }
+)
+
+BEDTools <- R6Class(
+  "BEDTools",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools",
+    setup_help_params = function() "--help",
+    setup_command_params = function(){
+      c(
+
+      )
+    }
+  )
+)

From 2a8218fe42c53f06bedafde1a3f38178c80dc19b Mon Sep 17 00:00:00 2001
From: wbq <2982433346@qq.com>
Date: Wed, 4 Jun 2025 00:13:11 +0800
Subject: [PATCH 02/10] add bedtools

---
 .Rhistory        |   0
 R/cmd-bedtools.R | 248 ++++++++++++++++++++++++++++++++++++++++++++---
 blit.Rproj       |   6 ++
 3 files changed, 238 insertions(+), 16 deletions(-)
 create mode 100644 .Rhistory

diff --git a/.Rhistory b/.Rhistory
new file mode 100644
index 0000000..e69de29
diff --git a/R/cmd-bedtools.R b/R/cmd-bedtools.R
index e27a7bb..1857db9 100644
--- a/R/cmd-bedtools.R
+++ b/R/cmd-bedtools.R
@@ -1,38 +1,254 @@
 #' Run bedtools
 #'
-#' The "bedtools" is a powerful toolset for genome arithmetic
+#' The `bedtools` is a powerful toolset for genome arithmetic,
+#' which includes `intersect`,`merge`,`coverage`,`getfasta`,`closest`,etc.
+#' @param file1 Path to bed/gff(gtf)/vcf/bam(sam) file.
+#' @param file2 Path to the second file, some commands require.
+#' @param ...
+#'  - `bedtools intersect`: `r rd_dots("bedtools intersect")`.
+#'  - `bedtools merge`: `r rd_dots("bedtools merge")`.
+#'  - `bedtools coverage`: `r rd_dots("bedtools coverage")`.
+#'  - `bedtools getfasta`: `r rd_dots("bedtools getfasta")`.
+#'  - `bedtools closest`: `r rd_dots("bedtools closest")`.
+#' @param ofile Path to the output file.
 #' @param
-#' @param ... 'r rd_dots("bedtools")'.
-#' @param
-#' @param bedtools 'r rd_cmd("bedtools")'.
-#' @family command
-#' @inherit exec return
+#'  - `bedtools intersect`: `r rd_cmd("bedtools intersect")`.
+#'  - `bedtools merge`: `r rd_cmd("bedtools merge")`.
+#'  - `bedtools coverage`: `r rd_cmd("bedtools coverage")`.
+#'  - `bedtools getfasta`: `r rd_cmd("bedtools getfasta")`.
+#'  - `bedtools closest`: `r rd_cmd("bedtools closest")`.
 #' @seealso
 #' - <https://github.com/arq5x/bedtools2/>
 #'
-#' 'r rd_seealso()'
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
 #' @export
-bedtools <- make_command(
-  "bedtools",
+
+#  bedtools intersect ----
+`bedtools intersect` <- make_command(
+  "bedtools intersect",
+  function(
+    file1,
+    file2,
+    ofile,
+    ...,
+    `bedtools intersect` = NULL
+  ){
+    assert_string(`bedtools intersect`, allow_empty = FALSE, allow_null = TRUE)
+    `BEDTools Intersect`$new(
+      cmd = `bedtools intersect`,
+      ...,
+      file1 = file1,
+      file2 = file2,
+      ofile = ofile,
+    )
+  }
+)
+
+`BEDTools Intersect` <- R6Class(
+  "BEDTools Intersect",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools intersect",
+    setup_help_params = function() "--help",
+    setup_command_params = function(file1, file2, ofile){
+      c(
+        arg0("-a", file1),
+        arg0("-b", file2),
+        arg0("-wa"),
+        arg0("-o", ofile),
+      )
+    }
+  )
+)
+
+#  bedtools merge ----
+`bedtools merge` <- make_command(
+  "bedtools merge",
+  function(
+    file1,
+    ofile,
+    ...,
+    dist = NULL,
+    `bedtools merge` = NULL
+  ){
+    assert_string(`bedtools merge`, allow_empty = FALSE, allow_null = TRUE)
+    `BEDTools Merge`$new(
+      cmd = `bedtools merge`,
+      ...,
+      file1 = file1,
+      dist = dist,
+      ofile = ofile,
+    )
+  }
+)
+
+`BEDTools Merge` <- R6Class(
+  "BEDTools Merge",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools merge",
+    setup_help_params = function() "--help",
+    setup_command_params = function(file1, dist, ofile){
+      c(
+        if (endsWith(file1, ".bed")|endsWith(file1, ".gff")){
+          arg0("-i", file1)
+        } else{
+          cli::cli_abort(
+            "{.arg file1} must be BED/GFF"
+          )
+        },
+        if (!is.null(dist)) arg0("-d", dist) else NULL,
+        arg0("-o", ofile),
+      )
+    }
+  )
+)
+
+#  bedtools coverage ----
+`bedtools coverage` <- make_command(
+  "bedtools coverage",
   function(
+    file1,
+    file2,
+    ofile,
+    ...,
+    `bedtools coverage` = NULL
+  ){
+    assert_string(`bedtools coverage`, allow_empty = FALSE, allow_null = TRUE)
+    `BEDTools Coverage`$new(
+      cmd = `bedtools coverage`,
+      ...,
+      file1 = file1,
+      file2 = file2,
+      ofile = ofile,
+    )
+  }
+)
+
+`BEDTools Coverage` <- R6Class(
+  "BEDTools Coverage",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools coverage",
+    setup_help_params = function() "--help",
+    setup_command_params = function(file1, file2, ofile){
+      c(
+        if (endsWith(file1, ".bed")|endsWith(file1, ".gff")){
+          arg0("-a", file1)
+        } else{
+          cli::cli_abort(
+            "{.arg file1} must be BED/GFF"
+          )
+        },
+        if (endsWith(file2, ".bed")|endsWith(file2, ".gff")|endsWith(file2, ".bam")){
+          arg0("-b", file2)
+        } else{
+          cli::cli_abort(
+            "{.arg file2} must be BED/GFF/BAM"
+          )
+        },
+        arg0("-o", ofile),
+      )
+    }
+  )
+)
 
+#  bedtools getfasta ----
+`bedtools getfasta` <- make_command(
+  "bedtools getfasta",
+  function(
+    file1,
+    file2,
+    ofile,
+    ...,
+    `bedtools getfasta` = NULL
   ){
-    assert_string(bedtools,allow_empty = FALSE, allow_null = TRUE)
-    BEDTools$new(
-      cmd = bedtools,
+    assert_string(`bedtools getfasta`, allow_empty = FALSE, allow_null = TRUE)
+    `BEDTools Getfasta`$new(
+      cmd = `bedtools getfasta`,
+      ...,
+      file1 = file1,
+      file2 = file2,
+      ofile = ofile,
     )
   }
 )
 
-BEDTools <- R6Class(
-  "BEDTools",
+`BEDTools Getfasta` <- R6Class(
+  "BEDTools Getfasta",
   inherit = Command,
   private = list(
-    alias = function() "bedtools",
+    alias = function() "bedtools getfasta",
     setup_help_params = function() "--help",
-    setup_command_params = function(){
+    setup_command_params = function(file1, file2, ofile){
       c(
+        if (endsWith(file1, ".fa")){
+          arg0("-fi", file1)
+          } else{
+            cli::cli_abort(
+              "{.arg file1} must be FASTA"
+            )
+          },
+        if (endsWith(file2, ".bed")|endsWith(file2, ".gff")){
+          arg0("-bed", file2)
+        } else{
+          cli::cli_abort(
+            "{.arg file2} must be BED/GFF"
+          )
+        },
+        arg0("-fo", ofile),
+      )
+    }
+  )
+)
+
+#  bedtools closest ----
+`bedtools closest` <- make_command(
+  "bedtools closest",
+  function(
+    file1,
+    file2,
+    ofile,
+    ...,
+    `bedtools closest` = NULL
+  ){
+    assert_string(`bedtools closest`, allow_empty = FALSE, allow_null = TRUE)
+    `BEDTools Closest`$new(
+      cmd = `bedtools closest`,
+      ...,
+      file1 = file1,
+      file2 = file2,
+      ofile = ofile,
+    )
+  }
+)
 
+`BEDTools Closest` <- R6Class(
+  "BEDTools Closest",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools closest",
+    setup_help_params = function() "--help",
+    setup_command_params = function(file1, file2, ofile){
+      c(
+        if (endsWith(file1, ".bed")|endsWith(file1, ".gff")|endsWith(file1, ".vcf")){
+          arg0("-a", file1)
+        } else{
+          cli::cli_abort(
+            "{.arg file1} must be BED/GFF/VCF"
+          )
+        },
+        if (endsWith(file2, ".bed")|endsWith(file2, ".gff")|endsWith(file2, ".vcf")){
+          arg0("-b", file2)
+        } else{
+          cli::cli_abort(
+            "{.arg file2} must be BED/GFF/VCF"
+          )
+        },
+        args("-D"),
+        arg0("-o", ofile),
       )
     }
   )
diff --git a/blit.Rproj b/blit.Rproj
index aaa62a5..268608d 100644
--- a/blit.Rproj
+++ b/blit.Rproj
@@ -1,12 +1,18 @@
 Version: 1.0
+ProjectId: 8959c0d9-c76c-4fa8-a50c-0dae5e78ec5f
 
 RestoreWorkspace: No
 SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
 Encoding: UTF-8
 
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 LineEndingConversion: Posix

From b3979fb460f422c445eeca0deee528a4271c025a Mon Sep 17 00:00:00 2001
From: wbq <2982433346@qq.com>
Date: Wed, 4 Jun 2025 16:18:21 +0800
Subject: [PATCH 03/10] add bedtools

---
 R/{cmd-bedtools.R => cmd-bedtools(1).R} | 63 ++++++++++++-------------
 R/cmd-bedtools(2).R                     | 59 +++++++++++++++++++++++
 2 files changed, 90 insertions(+), 32 deletions(-)
 rename R/{cmd-bedtools.R => cmd-bedtools(1).R} (85%)
 create mode 100644 R/cmd-bedtools(2).R

diff --git a/R/cmd-bedtools.R b/R/cmd-bedtools(1).R
similarity index 85%
rename from R/cmd-bedtools.R
rename to R/cmd-bedtools(1).R
index 1857db9..a96d6aa 100644
--- a/R/cmd-bedtools.R
+++ b/R/cmd-bedtools(1).R
@@ -1,7 +1,7 @@
 #' Run bedtools
 #'
 #' The `bedtools` is a powerful toolset for genome arithmetic,
-#' which includes `intersect`,`merge`,`coverage`,`getfasta`,`closest`,etc.
+#' which includes `intersect`, `merge`, `coverage`, `getfasta`, `closest`, etc.
 #' @param file1 Path to bed/gff(gtf)/vcf/bam(sam) file.
 #' @param file2 Path to the second file, some commands require.
 #' @param ...
@@ -24,10 +24,9 @@
 #' @inherit exec return
 #' @family command
 #' @export
-
-#  bedtools intersect ----
-`bedtools intersect` <- make_command(
-  "bedtools intersect",
+#  bedtools_intersect ----
+bedtools_intersect <- make_command(
+  "bedtools_intersect",
   function(
     file1,
     file2,
@@ -36,7 +35,7 @@
     `bedtools intersect` = NULL
   ){
     assert_string(`bedtools intersect`, allow_empty = FALSE, allow_null = TRUE)
-    `BEDTools Intersect`$new(
+    BEDTools_Intersect$new(
       cmd = `bedtools intersect`,
       ...,
       file1 = file1,
@@ -46,8 +45,8 @@
   }
 )
 
-`BEDTools Intersect` <- R6Class(
-  "BEDTools Intersect",
+BEDTools_Intersect <- R6Class(
+  "BEDTools_Intersect",
   inherit = Command,
   private = list(
     alias = function() "bedtools intersect",
@@ -63,9 +62,9 @@
   )
 )
 
-#  bedtools merge ----
-`bedtools merge` <- make_command(
-  "bedtools merge",
+#  bedtools_merge ----
+bedtools_merge <- make_command(
+  "bedtools_merge",
   function(
     file1,
     ofile,
@@ -74,7 +73,7 @@
     `bedtools merge` = NULL
   ){
     assert_string(`bedtools merge`, allow_empty = FALSE, allow_null = TRUE)
-    `BEDTools Merge`$new(
+    `BEDTools_Merge`$new(
       cmd = `bedtools merge`,
       ...,
       file1 = file1,
@@ -84,8 +83,8 @@
   }
 )
 
-`BEDTools Merge` <- R6Class(
-  "BEDTools Merge",
+BEDTools_Merge <- R6Class(
+  "BEDTools_Merge",
   inherit = Command,
   private = list(
     alias = function() "bedtools merge",
@@ -106,9 +105,9 @@
   )
 )
 
-#  bedtools coverage ----
-`bedtools coverage` <- make_command(
-  "bedtools coverage",
+#  bedtools_coverage ----
+bedtools_coverage <- make_command(
+  "bedtools_coverage",
   function(
     file1,
     file2,
@@ -117,7 +116,7 @@
     `bedtools coverage` = NULL
   ){
     assert_string(`bedtools coverage`, allow_empty = FALSE, allow_null = TRUE)
-    `BEDTools Coverage`$new(
+    BEDTools_Coverage$new(
       cmd = `bedtools coverage`,
       ...,
       file1 = file1,
@@ -127,8 +126,8 @@
   }
 )
 
-`BEDTools Coverage` <- R6Class(
-  "BEDTools Coverage",
+BEDTools_Coverage <- R6Class(
+  "BEDTools_Coverage",
   inherit = Command,
   private = list(
     alias = function() "bedtools coverage",
@@ -155,9 +154,9 @@
   )
 )
 
-#  bedtools getfasta ----
-`bedtools getfasta` <- make_command(
-  "bedtools getfasta",
+#  bedtools_getfasta ----
+bedtools_getfasta <- make_command(
+  "bedtools_getfasta",
   function(
     file1,
     file2,
@@ -166,7 +165,7 @@
     `bedtools getfasta` = NULL
   ){
     assert_string(`bedtools getfasta`, allow_empty = FALSE, allow_null = TRUE)
-    `BEDTools Getfasta`$new(
+    BEDTools_Getfasta$new(
       cmd = `bedtools getfasta`,
       ...,
       file1 = file1,
@@ -176,8 +175,8 @@
   }
 )
 
-`BEDTools Getfasta` <- R6Class(
-  "BEDTools Getfasta",
+BEDTools_Getfasta <- R6Class(
+  "BEDTools_Getfasta",
   inherit = Command,
   private = list(
     alias = function() "bedtools getfasta",
@@ -204,9 +203,9 @@
   )
 )
 
-#  bedtools closest ----
-`bedtools closest` <- make_command(
-  "bedtools closest",
+#  bedtools_closest ----
+bedtools_closest <- make_command(
+  "bedtools_closest",
   function(
     file1,
     file2,
@@ -215,7 +214,7 @@
     `bedtools closest` = NULL
   ){
     assert_string(`bedtools closest`, allow_empty = FALSE, allow_null = TRUE)
-    `BEDTools Closest`$new(
+    BEDTools_Closest$new(
       cmd = `bedtools closest`,
       ...,
       file1 = file1,
@@ -225,8 +224,8 @@
   }
 )
 
-`BEDTools Closest` <- R6Class(
-  "BEDTools Closest",
+BEDTools_Closest <- R6Class(
+  "BEDTools_Closest",
   inherit = Command,
   private = list(
     alias = function() "bedtools closest",
diff --git a/R/cmd-bedtools(2).R b/R/cmd-bedtools(2).R
new file mode 100644
index 0000000..6096e0d
--- /dev/null
+++ b/R/cmd-bedtools(2).R
@@ -0,0 +1,59 @@
+#' Run bedtools
+#'
+#' The `bedtools` is a powerful toolset for genome arithmetic.
+#' @param subcmd Sub-Command of bedtools. Details see: `r rd_help("bedtools")`.
+#' @param file1 Path to bed/gff(gtf)/vcf/bam(sam) file.
+#' @param file2 Path to the second file, some commands require.
+#' @param ... `r rd_dots("bedtools")`.
+#' @param ofile Path to the output file.
+#' @param bedtools `r rd_cmd("bedtools")`.
+#' @seealso
+#' - <https://github.com/arq5x/bedtools2/>
+#'
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
+#' @export
+bedtools <- make_command(
+  "bedtools",
+  function(
+    subcmd = NULL,
+    file1,
+    ofile,
+    ...,
+    file2 = NULL,
+    bedtools = NULL
+  ) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(bedtools, allow_empty = FALSE, allow_null = TRUE)
+    BEDTools$new(
+      cmd = bedtools,
+      ...,
+      subcmd = subcmd,
+      file1 = file1,
+      file2 = file2,
+      ofile = ofile
+    )
+  }
+)
+
+BEDTools <- R6Class(
+  "BEDTools",
+  inherit = Command,
+  private = list(
+    alias = function() "bedtools",
+    setup_help_params = function() "help",
+    combine_params = function(subcmd, file1, file2, ofile) {
+      c(
+        if (private$help) {
+          c(super$combine_params(), subcmd)
+        } else {
+          c(subcmd, super$combine_params())
+        },
+        arg0("-a", file1),
+        if (!is.null(file2)) arg0("-b", file2) else NULL,
+        arg0("-o", ofile),
+      )
+    }
+  )
+)

From 8320ab27391caa5892089bc75e99564bcefc4eb3 Mon Sep 17 00:00:00 2001
From: wbq <2982433346@qq.com>
Date: Wed, 4 Jun 2025 16:30:20 +0800
Subject: [PATCH 04/10] init

---
 R/{cmd-bedtools(2).R => cmd-bedtools.R}   | 0
 R/{cmd-bedtools(1).R => cmd-bedtools_1.R} | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename R/{cmd-bedtools(2).R => cmd-bedtools.R} (100%)
 rename R/{cmd-bedtools(1).R => cmd-bedtools_1.R} (100%)

diff --git a/R/cmd-bedtools(2).R b/R/cmd-bedtools.R
similarity index 100%
rename from R/cmd-bedtools(2).R
rename to R/cmd-bedtools.R
diff --git a/R/cmd-bedtools(1).R b/R/cmd-bedtools_1.R
similarity index 100%
rename from R/cmd-bedtools(1).R
rename to R/cmd-bedtools_1.R

From f8a11e2977ebeda680373745d148defbc46e6900 Mon Sep 17 00:00:00 2001
From: wbq <2982433346@qq.com>
Date: Thu, 5 Jun 2025 17:24:32 +0800
Subject: [PATCH 05/10] add document

---
 man/bedtools.Rd           | 54 ++++++++++++++++++++++++++++++++
 man/bedtools_intersect.Rd | 65 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 119 insertions(+)
 create mode 100644 man/bedtools.Rd
 create mode 100644 man/bedtools_intersect.Rd

diff --git a/man/bedtools.Rd b/man/bedtools.Rd
new file mode 100644
index 0000000..f32ccca
--- /dev/null
+++ b/man/bedtools.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cmd-bedtools.R
+\name{bedtools}
+\alias{bedtools}
+\title{Run bedtools}
+\usage{
+bedtools(subcmd = NULL, file1, ofile, ..., file2 = NULL, bedtools = NULL)
+}
+\arguments{
+\item{subcmd}{Sub-Command of bedtools. Details see: \code{cmd_help(bedtools())}.}
+
+\item{file1}{Path to bed/gff(gtf)/vcf/bam(sam) file.}
+
+\item{ofile}{Path to the output file.}
+
+\item{...}{<\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \code{bedtools} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \code{cmd_help(bedtools())}.}
+
+\item{file2}{Path to the second file, some commands require.}
+
+\item{bedtools}{A string of path to \code{bedtools} command.}
+}
+\value{
+A \code{command} object.
+}
+\description{
+The \code{bedtools} is a powerful toolset for genome arithmetic.
+}
+\seealso{
+\itemize{
+\item \url{https://github.com/arq5x/bedtools2/}
+\item \code{\link[=cmd_wd]{cmd_wd()}}/\code{\link[=cmd_envvar]{cmd_envvar()}}/\code{\link[=cmd_envpath]{cmd_envpath()}}/\code{\link[=cmd_condaenv]{cmd_condaenv()}}
+\item \code{\link[=cmd_on_start]{cmd_on_start()}}/\code{\link[=cmd_on_exit]{cmd_on_exit()}}
+\item \code{\link[=cmd_on_succeed]{cmd_on_succeed()}}/\code{\link[=cmd_on_fail]{cmd_on_fail()}}
+\item \code{\link[=cmd_parallel]{cmd_parallel()}}
+}
+
+Other \code{commands}:
+\code{\link{allele_counter}()},
+\code{\link{bedtools_intersect}()},
+\code{\link{cellranger}()},
+\code{\link{conda}()},
+\code{\link{fastp}()},
+\code{\link{fastq_pair}()},
+\code{\link{gistic2}()},
+\code{\link{kraken2}()},
+\code{\link{kraken_tools}()},
+\code{\link{perl}()},
+\code{\link{pyscenic}()},
+\code{\link{python}()},
+\code{\link{samtools}()},
+\code{\link{seqkit}()},
+\code{\link{trust4}()}
+}
+\concept{command}
diff --git a/man/bedtools_intersect.Rd b/man/bedtools_intersect.Rd
new file mode 100644
index 0000000..a7335c2
--- /dev/null
+++ b/man/bedtools_intersect.Rd
@@ -0,0 +1,65 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cmd-bedtools_1.R
+\name{bedtools_intersect}
+\alias{bedtools_intersect}
+\title{Run bedtools}
+\usage{
+bedtools_intersect(file1, file2, ofile, ..., `bedtools intersect` = NULL)
+}
+\arguments{
+\item{file1}{Path to bed/gff(gtf)/vcf/bam(sam) file.}
+
+\item{file2}{Path to the second file, some commands require.}
+
+\item{ofile}{Path to the output file.}
+
+\item{...}{\itemize{
+\item \verb{bedtools intersect}: <\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \verb{bedtools intersect} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \verb{cmd_help(bedtools intersect())}.
+\item \verb{bedtools merge}: <\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \verb{bedtools merge} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \verb{cmd_help(bedtools merge())}.
+\item \verb{bedtools coverage}: <\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \verb{bedtools coverage} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \verb{cmd_help(bedtools coverage())}.
+\item \verb{bedtools getfasta}: <\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \verb{bedtools getfasta} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \verb{cmd_help(bedtools getfasta())}.
+\item \verb{bedtools closest}: <\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \verb{bedtools closest} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \verb{cmd_help(bedtools closest())}.
+}}
+
+\item{-}{\verb{bedtools intersect}: A string of path to \verb{bedtools intersect} command.
+\itemize{
+\item \verb{bedtools merge}: A string of path to \verb{bedtools merge} command.
+\item \verb{bedtools coverage}: A string of path to \verb{bedtools coverage} command.
+\item \verb{bedtools getfasta}: A string of path to \verb{bedtools getfasta} command.
+\item \verb{bedtools closest}: A string of path to \verb{bedtools closest} command.
+}}
+}
+\value{
+A \code{command} object.
+}
+\description{
+The \code{bedtools} is a powerful toolset for genome arithmetic,
+which includes \code{intersect}, \code{merge}, \code{coverage}, \code{getfasta}, \code{closest}, etc.
+}
+\seealso{
+\itemize{
+\item \url{https://github.com/arq5x/bedtools2/}
+\item \code{\link[=cmd_wd]{cmd_wd()}}/\code{\link[=cmd_envvar]{cmd_envvar()}}/\code{\link[=cmd_envpath]{cmd_envpath()}}/\code{\link[=cmd_condaenv]{cmd_condaenv()}}
+\item \code{\link[=cmd_on_start]{cmd_on_start()}}/\code{\link[=cmd_on_exit]{cmd_on_exit()}}
+\item \code{\link[=cmd_on_succeed]{cmd_on_succeed()}}/\code{\link[=cmd_on_fail]{cmd_on_fail()}}
+\item \code{\link[=cmd_parallel]{cmd_parallel()}}
+}
+
+Other \code{commands}:
+\code{\link{allele_counter}()},
+\code{\link{bedtools}()},
+\code{\link{cellranger}()},
+\code{\link{conda}()},
+\code{\link{fastp}()},
+\code{\link{fastq_pair}()},
+\code{\link{gistic2}()},
+\code{\link{kraken2}()},
+\code{\link{kraken_tools}()},
+\code{\link{perl}()},
+\code{\link{pyscenic}()},
+\code{\link{python}()},
+\code{\link{samtools}()},
+\code{\link{seqkit}()},
+\code{\link{trust4}()}
+}
+\concept{command}

From b53e36cafe59e69acd27b163eac31972f513aa69 Mon Sep 17 00:00:00 2001
From: wbq <2982433346@qq.com>
Date: Sat, 7 Jun 2025 20:19:15 +0800
Subject: [PATCH 06/10] Made modifications

---
 NAMESPACE                  |   1 +
 R/cmd-bedtools.R           |  41 ++----
 R/cmd-bedtools_1.R         | 254 -------------------------------------
 blit.Rproj                 |   1 -
 man/allele_counter.Rd      |   1 +
 man/bedtools.Rd            |  10 +-
 man/bedtools_intersect.Rd  |  65 ----------
 man/cellranger.Rd          |   1 +
 man/conda.Rd               |   1 +
 man/exec.Rd                |   1 +
 man/fastp.Rd               |   1 +
 man/fastq_pair.Rd          |   1 +
 man/gistic2.Rd             |   1 +
 man/kraken2.Rd             |   1 +
 man/kraken_tools.Rd        |   1 +
 man/perl.Rd                |   1 +
 man/pyscenic.Rd            |   1 +
 man/python.Rd              |   1 +
 man/samtools.Rd            |   1 +
 man/seqkit.Rd              |   1 +
 man/trust4.Rd              |   1 +
 tests/testthat/test-exec.R |   5 +
 22 files changed, 33 insertions(+), 359 deletions(-)
 delete mode 100644 R/cmd-bedtools_1.R
 delete mode 100644 man/bedtools_intersect.Rd

diff --git a/NAMESPACE b/NAMESPACE
index ed26bd9..8888fe2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ export(appmamba)
 export(appmamba_rc)
 export(arg)
 export(arg0)
+export(bedtools)
 export(cellranger)
 export(cmd_background)
 export(cmd_conda)
diff --git a/R/cmd-bedtools.R b/R/cmd-bedtools.R
index 6096e0d..d6ba1bd 100644
--- a/R/cmd-bedtools.R
+++ b/R/cmd-bedtools.R
@@ -2,12 +2,10 @@
 #'
 #' The `bedtools` is a powerful toolset for genome arithmetic.
 #' @param subcmd Sub-Command of bedtools. Details see: `r rd_help("bedtools")`.
-#' @param file1 Path to bed/gff(gtf)/vcf/bam(sam) file.
-#' @param file2 Path to the second file, some commands require.
 #' @param ... `r rd_dots("bedtools")`.
-#' @param ofile Path to the output file.
 #' @param bedtools `r rd_cmd("bedtools")`.
 #' @seealso
+#' - <http://bedtools.readthedocs.io/>
 #' - <https://github.com/arq5x/bedtools2/>
 #'
 #' `r rd_seealso()`
@@ -16,24 +14,10 @@
 #' @export
 bedtools <- make_command(
   "bedtools",
-  function(
-    subcmd = NULL,
-    file1,
-    ofile,
-    ...,
-    file2 = NULL,
-    bedtools = NULL
-  ) {
+  function(subcmd = NULL, ..., bedtools = NULL) {
     assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
     assert_string(bedtools, allow_empty = FALSE, allow_null = TRUE)
-    BEDTools$new(
-      cmd = bedtools,
-      ...,
-      subcmd = subcmd,
-      file1 = file1,
-      file2 = file2,
-      ofile = ofile
-    )
+    BEDTools$new(cmd = bedtools, ..., subcmd = subcmd)
   }
 )
 
@@ -42,18 +26,13 @@ BEDTools <- R6Class(
   inherit = Command,
   private = list(
     alias = function() "bedtools",
-    setup_help_params = function() "help",
-    combine_params = function(subcmd, file1, file2, ofile) {
-      c(
-        if (private$help) {
-          c(super$combine_params(), subcmd)
-        } else {
-          c(subcmd, super$combine_params())
-        },
-        arg0("-a", file1),
-        if (!is.null(file2)) arg0("-b", file2) else NULL,
-        arg0("-o", ofile),
-      )
+    setup_help_params = function() "--help",
+    combine_params = function(subcmd) {
+      if (private$help) {
+        c(super$combine_params(), subcmd)
+      } else {
+        c(subcmd, super$combine_params())
+      }
     }
   )
 )
diff --git a/R/cmd-bedtools_1.R b/R/cmd-bedtools_1.R
deleted file mode 100644
index a96d6aa..0000000
--- a/R/cmd-bedtools_1.R
+++ /dev/null
@@ -1,254 +0,0 @@
-#' Run bedtools
-#'
-#' The `bedtools` is a powerful toolset for genome arithmetic,
-#' which includes `intersect`, `merge`, `coverage`, `getfasta`, `closest`, etc.
-#' @param file1 Path to bed/gff(gtf)/vcf/bam(sam) file.
-#' @param file2 Path to the second file, some commands require.
-#' @param ...
-#'  - `bedtools intersect`: `r rd_dots("bedtools intersect")`.
-#'  - `bedtools merge`: `r rd_dots("bedtools merge")`.
-#'  - `bedtools coverage`: `r rd_dots("bedtools coverage")`.
-#'  - `bedtools getfasta`: `r rd_dots("bedtools getfasta")`.
-#'  - `bedtools closest`: `r rd_dots("bedtools closest")`.
-#' @param ofile Path to the output file.
-#' @param
-#'  - `bedtools intersect`: `r rd_cmd("bedtools intersect")`.
-#'  - `bedtools merge`: `r rd_cmd("bedtools merge")`.
-#'  - `bedtools coverage`: `r rd_cmd("bedtools coverage")`.
-#'  - `bedtools getfasta`: `r rd_cmd("bedtools getfasta")`.
-#'  - `bedtools closest`: `r rd_cmd("bedtools closest")`.
-#' @seealso
-#' - <https://github.com/arq5x/bedtools2/>
-#'
-#' `r rd_seealso()`
-#' @inherit exec return
-#' @family command
-#' @export
-#  bedtools_intersect ----
-bedtools_intersect <- make_command(
-  "bedtools_intersect",
-  function(
-    file1,
-    file2,
-    ofile,
-    ...,
-    `bedtools intersect` = NULL
-  ){
-    assert_string(`bedtools intersect`, allow_empty = FALSE, allow_null = TRUE)
-    BEDTools_Intersect$new(
-      cmd = `bedtools intersect`,
-      ...,
-      file1 = file1,
-      file2 = file2,
-      ofile = ofile,
-    )
-  }
-)
-
-BEDTools_Intersect <- R6Class(
-  "BEDTools_Intersect",
-  inherit = Command,
-  private = list(
-    alias = function() "bedtools intersect",
-    setup_help_params = function() "--help",
-    setup_command_params = function(file1, file2, ofile){
-      c(
-        arg0("-a", file1),
-        arg0("-b", file2),
-        arg0("-wa"),
-        arg0("-o", ofile),
-      )
-    }
-  )
-)
-
-#  bedtools_merge ----
-bedtools_merge <- make_command(
-  "bedtools_merge",
-  function(
-    file1,
-    ofile,
-    ...,
-    dist = NULL,
-    `bedtools merge` = NULL
-  ){
-    assert_string(`bedtools merge`, allow_empty = FALSE, allow_null = TRUE)
-    `BEDTools_Merge`$new(
-      cmd = `bedtools merge`,
-      ...,
-      file1 = file1,
-      dist = dist,
-      ofile = ofile,
-    )
-  }
-)
-
-BEDTools_Merge <- R6Class(
-  "BEDTools_Merge",
-  inherit = Command,
-  private = list(
-    alias = function() "bedtools merge",
-    setup_help_params = function() "--help",
-    setup_command_params = function(file1, dist, ofile){
-      c(
-        if (endsWith(file1, ".bed")|endsWith(file1, ".gff")){
-          arg0("-i", file1)
-        } else{
-          cli::cli_abort(
-            "{.arg file1} must be BED/GFF"
-          )
-        },
-        if (!is.null(dist)) arg0("-d", dist) else NULL,
-        arg0("-o", ofile),
-      )
-    }
-  )
-)
-
-#  bedtools_coverage ----
-bedtools_coverage <- make_command(
-  "bedtools_coverage",
-  function(
-    file1,
-    file2,
-    ofile,
-    ...,
-    `bedtools coverage` = NULL
-  ){
-    assert_string(`bedtools coverage`, allow_empty = FALSE, allow_null = TRUE)
-    BEDTools_Coverage$new(
-      cmd = `bedtools coverage`,
-      ...,
-      file1 = file1,
-      file2 = file2,
-      ofile = ofile,
-    )
-  }
-)
-
-BEDTools_Coverage <- R6Class(
-  "BEDTools_Coverage",
-  inherit = Command,
-  private = list(
-    alias = function() "bedtools coverage",
-    setup_help_params = function() "--help",
-    setup_command_params = function(file1, file2, ofile){
-      c(
-        if (endsWith(file1, ".bed")|endsWith(file1, ".gff")){
-          arg0("-a", file1)
-        } else{
-          cli::cli_abort(
-            "{.arg file1} must be BED/GFF"
-          )
-        },
-        if (endsWith(file2, ".bed")|endsWith(file2, ".gff")|endsWith(file2, ".bam")){
-          arg0("-b", file2)
-        } else{
-          cli::cli_abort(
-            "{.arg file2} must be BED/GFF/BAM"
-          )
-        },
-        arg0("-o", ofile),
-      )
-    }
-  )
-)
-
-#  bedtools_getfasta ----
-bedtools_getfasta <- make_command(
-  "bedtools_getfasta",
-  function(
-    file1,
-    file2,
-    ofile,
-    ...,
-    `bedtools getfasta` = NULL
-  ){
-    assert_string(`bedtools getfasta`, allow_empty = FALSE, allow_null = TRUE)
-    BEDTools_Getfasta$new(
-      cmd = `bedtools getfasta`,
-      ...,
-      file1 = file1,
-      file2 = file2,
-      ofile = ofile,
-    )
-  }
-)
-
-BEDTools_Getfasta <- R6Class(
-  "BEDTools_Getfasta",
-  inherit = Command,
-  private = list(
-    alias = function() "bedtools getfasta",
-    setup_help_params = function() "--help",
-    setup_command_params = function(file1, file2, ofile){
-      c(
-        if (endsWith(file1, ".fa")){
-          arg0("-fi", file1)
-          } else{
-            cli::cli_abort(
-              "{.arg file1} must be FASTA"
-            )
-          },
-        if (endsWith(file2, ".bed")|endsWith(file2, ".gff")){
-          arg0("-bed", file2)
-        } else{
-          cli::cli_abort(
-            "{.arg file2} must be BED/GFF"
-          )
-        },
-        arg0("-fo", ofile),
-      )
-    }
-  )
-)
-
-#  bedtools_closest ----
-bedtools_closest <- make_command(
-  "bedtools_closest",
-  function(
-    file1,
-    file2,
-    ofile,
-    ...,
-    `bedtools closest` = NULL
-  ){
-    assert_string(`bedtools closest`, allow_empty = FALSE, allow_null = TRUE)
-    BEDTools_Closest$new(
-      cmd = `bedtools closest`,
-      ...,
-      file1 = file1,
-      file2 = file2,
-      ofile = ofile,
-    )
-  }
-)
-
-BEDTools_Closest <- R6Class(
-  "BEDTools_Closest",
-  inherit = Command,
-  private = list(
-    alias = function() "bedtools closest",
-    setup_help_params = function() "--help",
-    setup_command_params = function(file1, file2, ofile){
-      c(
-        if (endsWith(file1, ".bed")|endsWith(file1, ".gff")|endsWith(file1, ".vcf")){
-          arg0("-a", file1)
-        } else{
-          cli::cli_abort(
-            "{.arg file1} must be BED/GFF/VCF"
-          )
-        },
-        if (endsWith(file2, ".bed")|endsWith(file2, ".gff")|endsWith(file2, ".vcf")){
-          arg0("-b", file2)
-        } else{
-          cli::cli_abort(
-            "{.arg file2} must be BED/GFF/VCF"
-          )
-        },
-        args("-D"),
-        arg0("-o", ofile),
-      )
-    }
-  )
-)
diff --git a/blit.Rproj b/blit.Rproj
index 268608d..69fafd4 100644
--- a/blit.Rproj
+++ b/blit.Rproj
@@ -1,5 +1,4 @@
 Version: 1.0
-ProjectId: 8959c0d9-c76c-4fa8-a50c-0dae5e78ec5f
 
 RestoreWorkspace: No
 SaveWorkspace: No
diff --git a/man/allele_counter.Rd b/man/allele_counter.Rd
index af89e9b..7592dc9 100644
--- a/man/allele_counter.Rd
+++ b/man/allele_counter.Rd
@@ -43,6 +43,7 @@ between some other projects, specifically \code{AscatNGS} and \code{Battenberg}.
 }
 
 Other \code{commands}:
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/bedtools.Rd b/man/bedtools.Rd
index f32ccca..dcf66a9 100644
--- a/man/bedtools.Rd
+++ b/man/bedtools.Rd
@@ -4,19 +4,13 @@
 \alias{bedtools}
 \title{Run bedtools}
 \usage{
-bedtools(subcmd = NULL, file1, ofile, ..., file2 = NULL, bedtools = NULL)
+bedtools(subcmd = NULL, ..., bedtools = NULL)
 }
 \arguments{
 \item{subcmd}{Sub-Command of bedtools. Details see: \code{cmd_help(bedtools())}.}
 
-\item{file1}{Path to bed/gff(gtf)/vcf/bam(sam) file.}
-
-\item{ofile}{Path to the output file.}
-
 \item{...}{<\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \code{bedtools} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \code{cmd_help(bedtools())}.}
 
-\item{file2}{Path to the second file, some commands require.}
-
 \item{bedtools}{A string of path to \code{bedtools} command.}
 }
 \value{
@@ -27,6 +21,7 @@ The \code{bedtools} is a powerful toolset for genome arithmetic.
 }
 \seealso{
 \itemize{
+\item \url{http://bedtools.readthedocs.io/}
 \item \url{https://github.com/arq5x/bedtools2/}
 \item \code{\link[=cmd_wd]{cmd_wd()}}/\code{\link[=cmd_envvar]{cmd_envvar()}}/\code{\link[=cmd_envpath]{cmd_envpath()}}/\code{\link[=cmd_condaenv]{cmd_condaenv()}}
 \item \code{\link[=cmd_on_start]{cmd_on_start()}}/\code{\link[=cmd_on_exit]{cmd_on_exit()}}
@@ -36,7 +31,6 @@ The \code{bedtools} is a powerful toolset for genome arithmetic.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools_intersect}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/bedtools_intersect.Rd b/man/bedtools_intersect.Rd
deleted file mode 100644
index a7335c2..0000000
--- a/man/bedtools_intersect.Rd
+++ /dev/null
@@ -1,65 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cmd-bedtools_1.R
-\name{bedtools_intersect}
-\alias{bedtools_intersect}
-\title{Run bedtools}
-\usage{
-bedtools_intersect(file1, file2, ofile, ..., `bedtools intersect` = NULL)
-}
-\arguments{
-\item{file1}{Path to bed/gff(gtf)/vcf/bam(sam) file.}
-
-\item{file2}{Path to the second file, some commands require.}
-
-\item{ofile}{Path to the output file.}
-
-\item{...}{\itemize{
-\item \verb{bedtools intersect}: <\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \verb{bedtools intersect} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \verb{cmd_help(bedtools intersect())}.
-\item \verb{bedtools merge}: <\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \verb{bedtools merge} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \verb{cmd_help(bedtools merge())}.
-\item \verb{bedtools coverage}: <\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \verb{bedtools coverage} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \verb{cmd_help(bedtools coverage())}.
-\item \verb{bedtools getfasta}: <\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \verb{bedtools getfasta} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \verb{cmd_help(bedtools getfasta())}.
-\item \verb{bedtools closest}: <\link[rlang:dyn-dots]{dynamic dots}> Additional arguments passed to \verb{bedtools closest} command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using \code{\link[=shQuote]{shQuote()}}. Details see: \verb{cmd_help(bedtools closest())}.
-}}
-
-\item{-}{\verb{bedtools intersect}: A string of path to \verb{bedtools intersect} command.
-\itemize{
-\item \verb{bedtools merge}: A string of path to \verb{bedtools merge} command.
-\item \verb{bedtools coverage}: A string of path to \verb{bedtools coverage} command.
-\item \verb{bedtools getfasta}: A string of path to \verb{bedtools getfasta} command.
-\item \verb{bedtools closest}: A string of path to \verb{bedtools closest} command.
-}}
-}
-\value{
-A \code{command} object.
-}
-\description{
-The \code{bedtools} is a powerful toolset for genome arithmetic,
-which includes \code{intersect}, \code{merge}, \code{coverage}, \code{getfasta}, \code{closest}, etc.
-}
-\seealso{
-\itemize{
-\item \url{https://github.com/arq5x/bedtools2/}
-\item \code{\link[=cmd_wd]{cmd_wd()}}/\code{\link[=cmd_envvar]{cmd_envvar()}}/\code{\link[=cmd_envpath]{cmd_envpath()}}/\code{\link[=cmd_condaenv]{cmd_condaenv()}}
-\item \code{\link[=cmd_on_start]{cmd_on_start()}}/\code{\link[=cmd_on_exit]{cmd_on_exit()}}
-\item \code{\link[=cmd_on_succeed]{cmd_on_succeed()}}/\code{\link[=cmd_on_fail]{cmd_on_fail()}}
-\item \code{\link[=cmd_parallel]{cmd_parallel()}}
-}
-
-Other \code{commands}:
-\code{\link{allele_counter}()},
-\code{\link{bedtools}()},
-\code{\link{cellranger}()},
-\code{\link{conda}()},
-\code{\link{fastp}()},
-\code{\link{fastq_pair}()},
-\code{\link{gistic2}()},
-\code{\link{kraken2}()},
-\code{\link{kraken_tools}()},
-\code{\link{perl}()},
-\code{\link{pyscenic}()},
-\code{\link{python}()},
-\code{\link{samtools}()},
-\code{\link{seqkit}()},
-\code{\link{trust4}()}
-}
-\concept{command}
diff --git a/man/cellranger.Rd b/man/cellranger.Rd
index c6132c1..a147004 100644
--- a/man/cellranger.Rd
+++ b/man/cellranger.Rd
@@ -48,6 +48,7 @@ cellranger(
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
 \code{\link{fastq_pair}()},
diff --git a/man/conda.Rd b/man/conda.Rd
index 876b7ed..165cd39 100644
--- a/man/conda.Rd
+++ b/man/conda.Rd
@@ -29,6 +29,7 @@ Run conda
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{fastp}()},
 \code{\link{fastq_pair}()},
diff --git a/man/exec.Rd b/man/exec.Rd
index 64e7f40..8e0b526 100644
--- a/man/exec.Rd
+++ b/man/exec.Rd
@@ -21,6 +21,7 @@ Invoke a System Command
 
 \itemize{
 \item \code{\link[=allele_counter]{allele_counter()}}
+\item \code{\link[=bedtools]{bedtools()}}
 \item \code{\link[=cellranger]{cellranger()}}
 \item \code{\link[=conda]{conda()}}
 \item \code{\link[=fastp]{fastp()}}
diff --git a/man/fastp.Rd b/man/fastp.Rd
index 1be6075..765e0ef 100644
--- a/man/fastp.Rd
+++ b/man/fastp.Rd
@@ -33,6 +33,7 @@ and quality control for FastQ data.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastq_pair}()},
diff --git a/man/fastq_pair.Rd b/man/fastq_pair.Rd
index f432d1b..010a540 100644
--- a/man/fastq_pair.Rd
+++ b/man/fastq_pair.Rd
@@ -54,6 +54,7 @@ they demand paired end files have the same number of reads.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/gistic2.Rd b/man/gistic2.Rd
index 487a27e..7346991 100644
--- a/man/gistic2.Rd
+++ b/man/gistic2.Rd
@@ -51,6 +51,7 @@ deletion, and it lists genes found in each "wide peak" region.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/kraken2.Rd b/man/kraken2.Rd
index b4b9d49..b44a199 100644
--- a/man/kraken2.Rd
+++ b/man/kraken2.Rd
@@ -57,6 +57,7 @@ given k-mer.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/kraken_tools.Rd b/man/kraken_tools.Rd
index cf873d6..17ee478 100644
--- a/man/kraken_tools.Rd
+++ b/man/kraken_tools.Rd
@@ -33,6 +33,7 @@ analysis of Kraken results.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/perl.Rd b/man/perl.Rd
index 89eed70..0babc4f 100644
--- a/man/perl.Rd
+++ b/man/perl.Rd
@@ -30,6 +30,7 @@ years of development.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/pyscenic.Rd b/man/pyscenic.Rd
index db6b9dd..df7e0e9 100644
--- a/man/pyscenic.Rd
+++ b/man/pyscenic.Rd
@@ -30,6 +30,7 @@ Run pyscenic
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/python.Rd b/man/python.Rd
index 7b5c513..8bbb5af 100644
--- a/man/python.Rd
+++ b/man/python.Rd
@@ -30,6 +30,7 @@ systems more effectively.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/samtools.Rd b/man/samtools.Rd
index ed59740..ab889f6 100644
--- a/man/samtools.Rd
+++ b/man/samtools.Rd
@@ -32,6 +32,7 @@ systems more effectively.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/seqkit.Rd b/man/seqkit.Rd
index 6922f84..a6303b7 100644
--- a/man/seqkit.Rd
+++ b/man/seqkit.Rd
@@ -30,6 +30,7 @@ Run seqkit
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/trust4.Rd b/man/trust4.Rd
index ae887a7..c8cc737 100644
--- a/man/trust4.Rd
+++ b/man/trust4.Rd
@@ -85,6 +85,7 @@ data
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/tests/testthat/test-exec.R b/tests/testthat/test-exec.R
index acda33e..d0745e8 100644
--- 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()

From 1be2782d26de419068b3f549c7cb6d53a8de7f7b Mon Sep 17 00:00:00 2001
From: wbq <2982433346@qq.com>
Date: Sat, 7 Jun 2025 20:30:31 +0800
Subject: [PATCH 07/10] clean blit.Rproj

---
 blit.Rproj | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/blit.Rproj b/blit.Rproj
index 69fafd4..aaa62a5 100644
--- a/blit.Rproj
+++ b/blit.Rproj
@@ -5,13 +5,8 @@ SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
 Encoding: UTF-8
 
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 LineEndingConversion: Posix

From 94b49eec169da206735ece59005e538636a1afb7 Mon Sep 17 00:00:00 2001
From: wbq <2982433346@qq.com>
Date: Sat, 7 Jun 2025 20:43:32 +0800
Subject: [PATCH 08/10] clean man

---
 man/allele_counter.Rd | 1 -
 man/cellranger.Rd     | 1 -
 man/conda.Rd          | 1 -
 man/exec.Rd           | 1 -
 man/fastp.Rd          | 1 -
 man/fastq_pair.Rd     | 1 -
 man/gistic2.Rd        | 1 -
 man/kraken2.Rd        | 1 -
 man/kraken_tools.Rd   | 1 -
 man/perl.Rd           | 1 -
 man/pyscenic.Rd       | 1 -
 man/python.Rd         | 1 -
 man/samtools.Rd       | 1 -
 man/seqkit.Rd         | 1 -
 man/trust4.Rd         | 1 -
 15 files changed, 15 deletions(-)

diff --git a/man/allele_counter.Rd b/man/allele_counter.Rd
index 7592dc9..af89e9b 100644
--- a/man/allele_counter.Rd
+++ b/man/allele_counter.Rd
@@ -43,7 +43,6 @@ between some other projects, specifically \code{AscatNGS} and \code{Battenberg}.
 }
 
 Other \code{commands}:
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/cellranger.Rd b/man/cellranger.Rd
index a147004..c6132c1 100644
--- a/man/cellranger.Rd
+++ b/man/cellranger.Rd
@@ -48,7 +48,6 @@ cellranger(
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
 \code{\link{fastq_pair}()},
diff --git a/man/conda.Rd b/man/conda.Rd
index 165cd39..876b7ed 100644
--- a/man/conda.Rd
+++ b/man/conda.Rd
@@ -29,7 +29,6 @@ Run conda
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{fastp}()},
 \code{\link{fastq_pair}()},
diff --git a/man/exec.Rd b/man/exec.Rd
index 8e0b526..64e7f40 100644
--- a/man/exec.Rd
+++ b/man/exec.Rd
@@ -21,7 +21,6 @@ Invoke a System Command
 
 \itemize{
 \item \code{\link[=allele_counter]{allele_counter()}}
-\item \code{\link[=bedtools]{bedtools()}}
 \item \code{\link[=cellranger]{cellranger()}}
 \item \code{\link[=conda]{conda()}}
 \item \code{\link[=fastp]{fastp()}}
diff --git a/man/fastp.Rd b/man/fastp.Rd
index 765e0ef..1be6075 100644
--- a/man/fastp.Rd
+++ b/man/fastp.Rd
@@ -33,7 +33,6 @@ and quality control for FastQ data.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastq_pair}()},
diff --git a/man/fastq_pair.Rd b/man/fastq_pair.Rd
index 010a540..f432d1b 100644
--- a/man/fastq_pair.Rd
+++ b/man/fastq_pair.Rd
@@ -54,7 +54,6 @@ they demand paired end files have the same number of reads.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/gistic2.Rd b/man/gistic2.Rd
index 7346991..487a27e 100644
--- a/man/gistic2.Rd
+++ b/man/gistic2.Rd
@@ -51,7 +51,6 @@ deletion, and it lists genes found in each "wide peak" region.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/kraken2.Rd b/man/kraken2.Rd
index b44a199..b4b9d49 100644
--- a/man/kraken2.Rd
+++ b/man/kraken2.Rd
@@ -57,7 +57,6 @@ given k-mer.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/kraken_tools.Rd b/man/kraken_tools.Rd
index 17ee478..cf873d6 100644
--- a/man/kraken_tools.Rd
+++ b/man/kraken_tools.Rd
@@ -33,7 +33,6 @@ analysis of Kraken results.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/perl.Rd b/man/perl.Rd
index 0babc4f..89eed70 100644
--- a/man/perl.Rd
+++ b/man/perl.Rd
@@ -30,7 +30,6 @@ years of development.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/pyscenic.Rd b/man/pyscenic.Rd
index df7e0e9..db6b9dd 100644
--- a/man/pyscenic.Rd
+++ b/man/pyscenic.Rd
@@ -30,7 +30,6 @@ Run pyscenic
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/python.Rd b/man/python.Rd
index 8bbb5af..7b5c513 100644
--- a/man/python.Rd
+++ b/man/python.Rd
@@ -30,7 +30,6 @@ systems more effectively.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/samtools.Rd b/man/samtools.Rd
index ab889f6..ed59740 100644
--- a/man/samtools.Rd
+++ b/man/samtools.Rd
@@ -32,7 +32,6 @@ systems more effectively.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/seqkit.Rd b/man/seqkit.Rd
index a6303b7..6922f84 100644
--- a/man/seqkit.Rd
+++ b/man/seqkit.Rd
@@ -30,7 +30,6 @@ Run seqkit
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/trust4.Rd b/man/trust4.Rd
index c8cc737..ae887a7 100644
--- a/man/trust4.Rd
+++ b/man/trust4.Rd
@@ -85,7 +85,6 @@ data
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},

From ec0b97a8697222ce641c2d2b6a82600ceee3460d Mon Sep 17 00:00:00 2001
From: Yunuuuu <yunyunpp96@outlook.com>
Date: Fri, 19 Sep 2025 20:22:28 +0800
Subject: [PATCH 09/10] docs: update and regenerate package documentation with
 roxygen2

---
 NAMESPACE             | 2 +-
 man/allele_counter.Rd | 3 ++-
 man/bcftools.Rd       | 5 ++++-
 man/bedtools.Rd       | 6 +++++-
 man/bowtie2.Rd        | 6 +++++-
 man/cellranger.Rd     | 3 ++-
 man/conda.Rd          | 3 ++-
 man/exec.Rd           | 3 ++-
 man/fastp.Rd          | 3 ++-
 man/fastq_pair.Rd     | 3 ++-
 man/gistic2.Rd        | 3 ++-
 man/kraken2.Rd        | 3 ++-
 man/kraken_tools.Rd   | 3 ++-
 man/perl.Rd           | 3 ++-
 man/pyscenic.Rd       | 3 ++-
 man/python.Rd         | 3 ++-
 man/samtools.Rd       | 3 ++-
 man/seqkit.Rd         | 3 ++-
 man/snpEff.Rd         | 5 ++++-
 man/trust4.Rd         | 3 ++-
 man/varscan.Rd        | 4 ++++
 21 files changed, 53 insertions(+), 20 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 3b51689..8913399 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,9 +7,9 @@ export(appmamba)
 export(appmamba_rc)
 export(arg)
 export(arg0)
+export(bcftools)
 export(bedtools)
 export(bowtie2)
-export(bcftools)
 export(cellranger)
 export(cmd_background)
 export(cmd_conda)
diff --git a/man/allele_counter.Rd b/man/allele_counter.Rd
index ace7f44..cfa696b 100644
--- a/man/allele_counter.Rd
+++ b/man/allele_counter.Rd
@@ -43,8 +43,9 @@ between some other projects, specifically \code{AscatNGS} and \code{Battenberg}.
 }
 
 Other \code{commands}:
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/bcftools.Rd b/man/bcftools.Rd
index f117b3b..f884a5e 100644
--- a/man/bcftools.Rd
+++ b/man/bcftools.Rd
@@ -34,6 +34,8 @@ All commands work transparently with both VCFs and BCFs, both uncompressed and B
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
@@ -47,6 +49,7 @@ Other \code{commands}:
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
 \code{\link{snpEff}()},
-\code{\link{trust4}()}
+\code{\link{trust4}()},
+\code{\link{varscan}()}
 }
 \concept{command}
diff --git a/man/bedtools.Rd b/man/bedtools.Rd
index dcf66a9..869b61c 100644
--- a/man/bedtools.Rd
+++ b/man/bedtools.Rd
@@ -31,6 +31,8 @@ The \code{bedtools} is a powerful toolset for genome arithmetic.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bcftools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
@@ -43,6 +45,8 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
-\code{\link{trust4}()}
+\code{\link{snpEff}()},
+\code{\link{trust4}()},
+\code{\link{varscan}()}
 }
 \concept{command}
diff --git a/man/bowtie2.Rd b/man/bowtie2.Rd
index 6d0563b..361c175 100644
--- a/man/bowtie2.Rd
+++ b/man/bowtie2.Rd
@@ -40,6 +40,8 @@ Bowtie 2 supports gapped, local, and paired-end alignment modes.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bcftools}()},
+\code{\link{bedtools}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
@@ -52,6 +54,8 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
-\code{\link{trust4}()}
+\code{\link{snpEff}()},
+\code{\link{trust4}()},
+\code{\link{varscan}()}
 }
 \concept{command}
diff --git a/man/cellranger.Rd b/man/cellranger.Rd
index 576a6b1..f52c025 100644
--- a/man/cellranger.Rd
+++ b/man/cellranger.Rd
@@ -48,8 +48,9 @@ cellranger(
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
 \code{\link{fastq_pair}()},
diff --git a/man/conda.Rd b/man/conda.Rd
index 9efe8f8..9fe0555 100644
--- a/man/conda.Rd
+++ b/man/conda.Rd
@@ -29,8 +29,9 @@ Run conda
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{fastp}()},
 \code{\link{fastq_pair}()},
diff --git a/man/exec.Rd b/man/exec.Rd
index 8cf83ce..31fb607 100644
--- a/man/exec.Rd
+++ b/man/exec.Rd
@@ -21,8 +21,9 @@ Invoke a System Command
 
 \itemize{
 \item \code{\link[=allele_counter]{allele_counter()}}
-\item \code{\link[=bowtie2]{bowtie2()}}
 \item \code{\link[=bcftools]{bcftools()}}
+\item \code{\link[=bedtools]{bedtools()}}
+\item \code{\link[=bowtie2]{bowtie2()}}
 \item \code{\link[=cellranger]{cellranger()}}
 \item \code{\link[=conda]{conda()}}
 \item \code{\link[=fastp]{fastp()}}
diff --git a/man/fastp.Rd b/man/fastp.Rd
index 46225c3..ec3e879 100644
--- a/man/fastp.Rd
+++ b/man/fastp.Rd
@@ -33,8 +33,9 @@ and quality control for FastQ data.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastq_pair}()},
diff --git a/man/fastq_pair.Rd b/man/fastq_pair.Rd
index 48dcb9b..3764bc6 100644
--- a/man/fastq_pair.Rd
+++ b/man/fastq_pair.Rd
@@ -54,8 +54,9 @@ they demand paired end files have the same number of reads.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/gistic2.Rd b/man/gistic2.Rd
index e800cef..42e9a6a 100644
--- a/man/gistic2.Rd
+++ b/man/gistic2.Rd
@@ -51,8 +51,9 @@ deletion, and it lists genes found in each "wide peak" region.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/kraken2.Rd b/man/kraken2.Rd
index 49efc23..0a1adc0 100644
--- a/man/kraken2.Rd
+++ b/man/kraken2.Rd
@@ -57,8 +57,9 @@ given k-mer.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/kraken_tools.Rd b/man/kraken_tools.Rd
index 3e6886c..fece02b 100644
--- a/man/kraken_tools.Rd
+++ b/man/kraken_tools.Rd
@@ -33,8 +33,9 @@ analysis of Kraken results.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/perl.Rd b/man/perl.Rd
index bf68f86..c2b8c8e 100644
--- a/man/perl.Rd
+++ b/man/perl.Rd
@@ -30,8 +30,9 @@ years of development.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/pyscenic.Rd b/man/pyscenic.Rd
index 5e2d739..63f20fc 100644
--- a/man/pyscenic.Rd
+++ b/man/pyscenic.Rd
@@ -30,8 +30,9 @@ Run pyscenic
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/python.Rd b/man/python.Rd
index 7e99e12..d4e32a3 100644
--- a/man/python.Rd
+++ b/man/python.Rd
@@ -30,8 +30,9 @@ systems more effectively.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/samtools.Rd b/man/samtools.Rd
index e5db7e1..5b1c133 100644
--- a/man/samtools.Rd
+++ b/man/samtools.Rd
@@ -32,8 +32,9 @@ systems more effectively.
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/seqkit.Rd b/man/seqkit.Rd
index 2685649..fcfe722 100644
--- a/man/seqkit.Rd
+++ b/man/seqkit.Rd
@@ -30,8 +30,9 @@ Run seqkit
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/snpEff.Rd b/man/snpEff.Rd
index 6c6a500..79b611a 100644
--- a/man/snpEff.Rd
+++ b/man/snpEff.Rd
@@ -33,6 +33,8 @@ It annotates and predicts the effects of genetic variants on genes and proteins
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
@@ -45,6 +47,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
-\code{\link{trust4}()}
+\code{\link{trust4}()},
+\code{\link{varscan}()}
 }
 \concept{command}
diff --git a/man/trust4.Rd b/man/trust4.Rd
index 62f2155..cdcc7bd 100644
--- a/man/trust4.Rd
+++ b/man/trust4.Rd
@@ -85,8 +85,9 @@ data
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
-\code{\link{bowtie2}()},
 \code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
diff --git a/man/varscan.Rd b/man/varscan.Rd
index 791ea29..03ae011 100644
--- a/man/varscan.Rd
+++ b/man/varscan.Rd
@@ -32,6 +32,9 @@ developed at the Genome Institute at Washington University to detect variants in
 
 Other \code{commands}:
 \code{\link{allele_counter}()},
+\code{\link{bcftools}()},
+\code{\link{bedtools}()},
+\code{\link{bowtie2}()},
 \code{\link{cellranger}()},
 \code{\link{conda}()},
 \code{\link{fastp}()},
@@ -44,6 +47,7 @@ Other \code{commands}:
 \code{\link{python}()},
 \code{\link{samtools}()},
 \code{\link{seqkit}()},
+\code{\link{snpEff}()},
 \code{\link{trust4}()}
 }
 \concept{command}

From 72c1685ad0643c999f0a4edb11de8413e0ae6718 Mon Sep 17 00:00:00 2001
From: Yunuuuu <yunyunpp96@outlook.com>
Date: Fri, 19 Sep 2025 20:28:49 +0800
Subject: [PATCH 10/10] refactor: remove Rhistory

---
 .Rhistory  | 0
 .gitignore | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 delete mode 100644 .Rhistory

diff --git a/.Rhistory b/.Rhistory
deleted file mode 100644
index e69de29..0000000
diff --git a/.gitignore b/.gitignore
index 6a6b6d8..6959d3c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,7 @@
 .Rproj.user
+.Rhistory
 .radian_history
 Scratch.RConsole
-
 /.quarto/
 README.html
 docs