From feb710ab538d1bf67ece3617739be738e7eb0663 Mon Sep 17 00:00:00 2001
From: roc-002 <3507755728@qq.com>
Date: Wed, 4 Jun 2025 16:00:05 +0800
Subject: [PATCH 01/10] init

---
 R/cmd-bwa.R               | 53 +++++++++++++++++++++++++++++++++++++++
 tests/testthat/test-bwa.R |  3 +++
 2 files changed, 56 insertions(+)
 create mode 100644 R/cmd-bwa.R
 create mode 100644 tests/testthat/test-bwa.R

diff --git a/R/cmd-bwa.R b/R/cmd-bwa.R
new file mode 100644
index 0000000..17273b4
--- /dev/null
+++ b/R/cmd-bwa.R
@@ -0,0 +1,53 @@
+#' Run fastp
+#'
+#' The `fastp` is a tool designed to provide ultrafast all-in-one preprocessing
+#' and quality control for FastQ data.
+#' @param fq1,fq2 A string of fastq file path.
+#' @param ... `r rd_dots("fastp")`.
+#' @param ofile1,ofile2 A string of path to the output fastq file.
+#' @param fastp `r rd_cmd("fastp")`.
+#' @family command
+#' @inherit exec return
+#' @seealso
+#' - <https://github.com/OpenGene/fastp>
+#'
+#' `r rd_seealso()`
+#' @export
+fastp <- make_command(
+  "fastp",
+  function(
+    fq1,
+    ofile1,
+    ...,
+    fq2 = NULL,
+    ofile2 = NULL,
+    fastp = NULL
+  ){
+    assert_string(fastp, allow_empty = FALSE, allow_null = TRUE)
+    Fastp$new(
+      cmd = fastp,
+      ...,
+      fq1 = fq1,
+      fq2 = fq2,
+      ofile1 = ofile1,
+      ofile2 = ofile2
+    )
+  }
+)
+
+Fastp <- R6Class(
+  "Fastp",
+  inherit = Command,
+  private = list(
+    alias = function() "fastp",
+    setup_help_params = function() "--help",
+    setup_command_params = function(fq1, fq2, ofile1, ofile2){
+      c(
+        arg0("-i", fq1),
+        if (!is.null(fq2)) arg0("-I", fq2) else NULL,
+        arg0("-o", ofile1),
+        if (!is.null(ofile2)) arg0("-O", ofile2) else NULL
+      )
+    }
+  )
+)
diff --git a/tests/testthat/test-bwa.R b/tests/testthat/test-bwa.R
new file mode 100644
index 0000000..1eaff3b
--- /dev/null
+++ b/tests/testthat/test-bwa.R
@@ -0,0 +1,3 @@
+testthat::test_that("`BlitProcess` stdin works well", {
+
+})

From dfe8f87f536d269fac5d3488415a7d9c040ccb67 Mon Sep 17 00:00:00 2001
From: roc-002 <3507755728@qq.com>
Date: Wed, 4 Jun 2025 16:09:51 +0800
Subject: [PATCH 02/10] rename fastp to bwa for a test

---
 R/cmd-bwa.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cmd-bwa.R b/R/cmd-bwa.R
index 17273b4..21e2823 100644
--- a/R/cmd-bwa.R
+++ b/R/cmd-bwa.R
@@ -1,4 +1,4 @@
-#' Run fastp
+#' Run bwa
 #'
 #' The `fastp` is a tool designed to provide ultrafast all-in-one preprocessing
 #' and quality control for FastQ data.

From 4c27cf3e3710487d3b5859870585a97a48ac94d8 Mon Sep 17 00:00:00 2001
From: roc-002 <3507755728@qq.com>
Date: Tue, 10 Jun 2025 18:43:08 +0800
Subject: [PATCH 03/10] add bwa

---
 R/cmd-bwa.R | 71 +++++++++++++++++++++++++----------------------------
 1 file changed, 33 insertions(+), 38 deletions(-)

diff --git a/R/cmd-bwa.R b/R/cmd-bwa.R
index 21e2823..000e90c 100644
--- a/R/cmd-bwa.R
+++ b/R/cmd-bwa.R
@@ -1,53 +1,48 @@
-#' Run bwa
+#' Run BWA
 #'
-#' The `fastp` is a tool designed to provide ultrafast all-in-one preprocessing
-#' and quality control for FastQ data.
-#' @param fq1,fq2 A string of fastq file path.
-#' @param ... `r rd_dots("fastp")`.
-#' @param ofile1,ofile2 A string of path to the output fastq file.
-#' @param fastp `r rd_cmd("fastp")`.
-#' @family command
+#' @param subcmd Sub-Command of BWA (e.g., "index", "mem").
+#' @param ... `r rd_dots("bwa")`.
+#' @param bwa `r rd_cmd("bwa")`.
 #' @inherit exec return
 #' @seealso
-#' - <https://github.com/OpenGene/fastp>
+#' - <http://bio-bwa.sourceforge.net/>
 #'
 #' `r rd_seealso()`
+#' @examples# 索引参考基因组
+#bwa("index", "-a", "bwtsw", "reference.fa")$run()
+
+# 序列比对
+#bwa("mem",
+#    "-t", "4"
+#    "reference.fa"
+#    "read1.fq"
+#    "read2.fq")$run(stdout = "output.sam")
+#' \dontrun{
+#' # 建立索引
+#' bwa("index", "-a", "bwtsw", "reference.fa")$run()
+#'
+#' # 双端序列比对
+#' bwa("mem", "-t", "4", "reference.fa", "read1.fq", "read2.fq")$run(stdout = "output.sam")
+#' }
+#' @family command
 #' @export
-fastp <- make_command(
-  "fastp",
-  function(
-    fq1,
-    ofile1,
-    ...,
-    fq2 = NULL,
-    ofile2 = NULL,
-    fastp = NULL
-  ){
-    assert_string(fastp, allow_empty = FALSE, allow_null = TRUE)
-    Fastp$new(
-      cmd = fastp,
-      ...,
-      fq1 = fq1,
-      fq2 = fq2,
-      ofile1 = ofile1,
-      ofile2 = ofile2
-    )
+bwa <- make_command(
+  "bwa",
+  function(subcmd = NULL, ..., bwa = NULL) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(bwa, allow_empty = FALSE, allow_null = TRUE)
+    BWA$new(cmd = bwa, ..., subcmd = subcmd)
   }
 )
 
-Fastp <- R6Class(
-  "Fastp",
+BWA <- R6Class(
+  "BWA",
   inherit = Command,
   private = list(
-    alias = function() "fastp",
+    alias = function() "bwa",
     setup_help_params = function() "--help",
-    setup_command_params = function(fq1, fq2, ofile1, ofile2){
-      c(
-        arg0("-i", fq1),
-        if (!is.null(fq2)) arg0("-I", fq2) else NULL,
-        arg0("-o", ofile1),
-        if (!is.null(ofile2)) arg0("-O", ofile2) else NULL
-      )
+    combine_params = function(subcmd) {
+      c(subcmd, super$combine_params())
     }
   )
 )

From 3fbeef12203acc8bae754bc1c1dc7875a9c6900d Mon Sep 17 00:00:00 2001
From: roc-002 <3507755728@qq.com>
Date: Thu, 12 Jun 2025 21:59:28 +0800
Subject: [PATCH 04/10] add discription

---
 R/cmd-bwa.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/cmd-bwa.R b/R/cmd-bwa.R
index 000e90c..4fc5adf 100644
--- a/R/cmd-bwa.R
+++ b/R/cmd-bwa.R
@@ -1,8 +1,11 @@
 #' Run BWA
 #'
+#'BWA is a software package that aligns low-divergence sequences to a
+#'large reference genome, such as the human genome
 #' @param subcmd Sub-Command of BWA (e.g., "index", "mem").
 #' @param ... `r rd_dots("bwa")`.
 #' @param bwa `r rd_cmd("bwa")`.
+#' @family command
 #' @inherit exec return
 #' @seealso
 #' - <http://bio-bwa.sourceforge.net/>

From 7e652cf8877e67addd49d9b6576b586c4c2a94f2 Mon Sep 17 00:00:00 2001
From: roc-002 <3507755728@qq.com>
Date: Fri, 13 Jun 2025 15:05:37 +0800
Subject: [PATCH 05/10] add test

---
 tests/testthat/test-bwa.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-bwa.R b/tests/testthat/test-bwa.R
index 1eaff3b..376ef5d 100644
--- a/tests/testthat/test-bwa.R
+++ b/tests/testthat/test-bwa.R
@@ -1,3 +1,7 @@
-testthat::test_that("`BlitProcess` stdin works well", {
+testthat::test_that("`bwa()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("bwa")))  # 确保系统安装了BWA
+  bwa() |> cmd_help()
 
+  bwa("index") |> cmd_help()
+  bwa("mem") |> cmd_help()
 })

From e46bd537f17a4af6d9ea463a0dfa74148de1f846 Mon Sep 17 00:00:00 2001
From: roc-002 <3507755728@qq.com>
Date: Fri, 13 Jun 2025 22:24:56 +0800
Subject: [PATCH 06/10] test

---
 blit.Rproj                | 5 +++++
 tests/testthat/test-bwa.R | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/blit.Rproj b/blit.Rproj
index aaa62a5..69fafd4 100644
--- a/blit.Rproj
+++ b/blit.Rproj
@@ -5,8 +5,13 @@ SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
 Encoding: UTF-8
 
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 LineEndingConversion: Posix
diff --git a/tests/testthat/test-bwa.R b/tests/testthat/test-bwa.R
index 376ef5d..301c576 100644
--- a/tests/testthat/test-bwa.R
+++ b/tests/testthat/test-bwa.R
@@ -1,5 +1,5 @@
 testthat::test_that("`bwa()` works as expected", {
-  testthat::skip_if_not(nzchar(Sys.which("bwa")))  # 确保系统安装了BWA
+  testthat::skip_if_not(nzchar(Sys.which("bwa")))
   bwa() |> cmd_help()
 
   bwa("index") |> cmd_help()

From 9281884f0cdfa7dfc850b60b3d0c027288a68eff Mon Sep 17 00:00:00 2001
From: roc-002 <3507755728@qq.com>
Date: Fri, 13 Jun 2025 22:29:56 +0800
Subject: [PATCH 07/10] test

---
 tests/testthat/test-bwa.R  | 7 -------
 tests/testthat/test-exec.R | 8 ++++++++
 2 files changed, 8 insertions(+), 7 deletions(-)
 delete mode 100644 tests/testthat/test-bwa.R

diff --git a/tests/testthat/test-bwa.R b/tests/testthat/test-bwa.R
deleted file mode 100644
index 301c576..0000000
--- a/tests/testthat/test-bwa.R
+++ /dev/null
@@ -1,7 +0,0 @@
-testthat::test_that("`bwa()` works as expected", {
-  testthat::skip_if_not(nzchar(Sys.which("bwa")))
-  bwa() |> cmd_help()
-
-  bwa("index") |> cmd_help()
-  bwa("mem") |> cmd_help()
-})
diff --git a/tests/testthat/test-exec.R b/tests/testthat/test-exec.R
index acda33e..b6dcc5e 100644
--- a/tests/testthat/test-exec.R
+++ b/tests/testthat/test-exec.R
@@ -3,6 +3,14 @@ testthat::test_that("`allele_counter()` works as expected", {
     allele_counter() |> cmd_help()
 })
 
+testthat::test_that("`bwa()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("bwa")))
+  bwa() |> cmd_help()
+
+  bwa("index") |> cmd_help()
+  bwa("mem") |> cmd_help()
+})
+
 testthat::test_that("`cellranger()` works as expected", {
     testthat::skip_if_not(nzchar(Sys.which("cellranger")))
     cellranger() |> cmd_help()

From 316ac05351c4b686e993f4656bc56d7182b4a26e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=81=E5=8A=A0?= <jiading682@qq.com>
Date: Mon, 8 Sep 2025 13:11:09 +0800
Subject: [PATCH 08/10] Update cmd-bwa.R

---
 R/cmd-bwa.R | 21 ++++++++-------------
 1 file changed, 8 insertions(+), 13 deletions(-)

diff --git a/R/cmd-bwa.R b/R/cmd-bwa.R
index 4fc5adf..41701da 100644
--- a/R/cmd-bwa.R
+++ b/R/cmd-bwa.R
@@ -1,7 +1,7 @@
 #' Run BWA
 #'
-#'BWA is a software package that aligns low-divergence sequences to a
-#'large reference genome, such as the human genome
+#' BWA is a software package that aligns low-divergence sequences to a
+#' large reference genome, such as the human genome
 #' @param subcmd Sub-Command of BWA (e.g., "index", "mem").
 #' @param ... `r rd_dots("bwa")`.
 #' @param bwa `r rd_cmd("bwa")`.
@@ -11,21 +11,16 @@
 #' - <http://bio-bwa.sourceforge.net/>
 #'
 #' `r rd_seealso()`
-#' @examples# 索引参考基因组
-#bwa("index", "-a", "bwtsw", "reference.fa")$run()
-
-# 序列比对
-#bwa("mem",
-#    "-t", "4"
-#    "reference.fa"
-#    "read1.fq"
-#    "read2.fq")$run(stdout = "output.sam")
+#' @examples
 #' \dontrun{
-#' # 建立索引
+#' # Index reference genome
 #' bwa("index", "-a", "bwtsw", "reference.fa")$run()
 #'
-#' # 双端序列比对
+#' # Paired-end sequence alignment
 #' bwa("mem", "-t", "4", "reference.fa", "read1.fq", "read2.fq")$run(stdout = "output.sam")
+#'
+#' # Single-end alignment (generate sai file)
+#' bwa("aln", "-t", "4", "reference.fa", "read.fq")$run(stdout = "read.sai")
 #' }
 #' @family command
 #' @export

From 5685498c6f169118bf7841089f48abf220859fd8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E4=B8=81=E5=8A=A0?= <jiading682@qq.com>
Date: Mon, 8 Sep 2025 13:12:14 +0800
Subject: [PATCH 09/10] Update test-exec.R

---
 tests/testthat/test-exec.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-exec.R b/tests/testthat/test-exec.R
index b6dcc5e..98129a2 100644
--- a/tests/testthat/test-exec.R
+++ b/tests/testthat/test-exec.R
@@ -6,7 +6,6 @@ testthat::test_that("`allele_counter()` works as expected", {
 testthat::test_that("`bwa()` works as expected", {
   testthat::skip_if_not(nzchar(Sys.which("bwa")))
   bwa() |> cmd_help()
-
   bwa("index") |> cmd_help()
   bwa("mem") |> cmd_help()
 })

From 3c7f1639495c4e7373667bf2b9980ad2b655e2e2 Mon Sep 17 00:00:00 2001
From: Yunuuuu <yunyunpp96@outlook.com>
Date: Fri, 19 Sep 2025 20:38:23 +0800
Subject: [PATCH 10/10] docs: use cmd_run() to execute commands

---
 R/cmd-bwa.R | 10 ++++++----
 man/bwa.Rd  | 30 ++++++------------------------
 2 files changed, 12 insertions(+), 28 deletions(-)

diff --git a/R/cmd-bwa.R b/R/cmd-bwa.R
index 41701da..d83b343 100644
--- a/R/cmd-bwa.R
+++ b/R/cmd-bwa.R
@@ -5,7 +5,6 @@
 #' @param subcmd Sub-Command of BWA (e.g., "index", "mem").
 #' @param ... `r rd_dots("bwa")`.
 #' @param bwa `r rd_cmd("bwa")`.
-#' @family command
 #' @inherit exec return
 #' @seealso
 #' - <http://bio-bwa.sourceforge.net/>
@@ -14,13 +13,16 @@
 #' @examples
 #' \dontrun{
 #' # Index reference genome
-#' bwa("index", "-a", "bwtsw", "reference.fa")$run()
+#' bwa("index", "-a", "bwtsw", "reference.fa") |>
+#'   cmd_run()
 #'
 #' # Paired-end sequence alignment
-#' bwa("mem", "-t", "4", "reference.fa", "read1.fq", "read2.fq")$run(stdout = "output.sam")
+#' bwa("mem", "-t", "4", "reference.fa", "read1.fq", "read2.fq") |>
+#'   cmd_run(stdout = "output.sam")
 #'
 #' # Single-end alignment (generate sai file)
-#' bwa("aln", "-t", "4", "reference.fa", "read.fq")$run(stdout = "read.sai")
+#' bwa("aln", "-t", "4", "reference.fa", "read.fq") |>
+#'   cmd_run(stdout = "read.sai")
 #' }
 #' @family command
 #' @export
diff --git a/man/bwa.Rd b/man/bwa.Rd
index dd8038b..908161b 100644
--- a/man/bwa.Rd
+++ b/man/bwa.Rd
@@ -23,13 +23,16 @@ large reference genome, such as the human genome
 \examples{
 \dontrun{
 # Index reference genome
-bwa("index", "-a", "bwtsw", "reference.fa")$run()
+bwa("index", "-a", "bwtsw", "reference.fa") |>
+  cmd_run()
 
 # Paired-end sequence alignment
-bwa("mem", "-t", "4", "reference.fa", "read1.fq", "read2.fq")$run(stdout = "output.sam")
+bwa("mem", "-t", "4", "reference.fa", "read1.fq", "read2.fq") |>
+  cmd_run(stdout = "output.sam")
 
 # Single-end alignment (generate sai file)
-bwa("aln", "-t", "4", "reference.fa", "read.fq")$run(stdout = "read.sai")
+bwa("aln", "-t", "4", "reference.fa", "read.fq") |>
+  cmd_run(stdout = "read.sai")
 }
 }
 \seealso{
@@ -41,27 +44,6 @@ bwa("aln", "-t", "4", "reference.fa", "read.fq")$run(stdout = "read.sai")
 \item \code{\link[=cmd_parallel]{cmd_parallel()}}
 }
 
-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}()},
-\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{snpEff}()},
-\code{\link{trust4}()},
-\code{\link{varscan}()}
-
 Other \code{commands}:
 \code{\link{allele_counter}()},
 \code{\link{bcftools}()},