WangLabCSU · ShixiangWang · Sep 7, 2025 · Jul 5, 2025 · Jul 5, 2025 · Jul 5, 2025
diff --git a/NAMESPACE b/NAMESPACE
@@ -37,6 +37,7 @@ export(pyscenic)
 export(python)
 export(samtools)
 export(seqkit)
+export(snpEff)
 export(trust4)
 export(trust4_gene_names)
 export(trust4_imgt_annot)

diff --git a/R/cmd-snpEff.R b/R/cmd-snpEff.R
@@ -0,0 +1,37 @@
+#' Genetic variant annotation, and functional effect prediction toolbox. 
+#' It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
+#'
+#' @param subcmd Sub-Command of snpEff. Details see: `r rd_help("snpEff")`.
+#' @param ... `r rd_dots("snpEff")`.
+#' @param snpEff `r rd_cmd("snpEff")`.
+#' @seealso
+#' - <https://pcingola.github.io/SnpEff/>
+#'
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
+#' @export
+snpEff <- make_command(
+  "snpEff",
+  function(subcmd = NULL, ..., snpEff = NULL) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(snpEff, allow_empty = FALSE, allow_null = TRUE)
+    SnpEff$new(cmd = snpEff, ..., subcmd = subcmd)
+  }
+)
+
+SnpEff <- R6Class(
+  "SnpEff",
+  inherit = Command,
+  private = list(
+    alias = function() "snpEff",
+    setup_help_params = function() "help",
+    combine_params = function(subcmd) {
+      if (private$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/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