add freebayes

Author: SunPast

NAMESPACE

@@ -30,6 +30,7 @@ export(exec)
 export(fastp)
 export(fastq_pair)
 export(fastq_read_pair)
+export(freebayes)
 export(gistic2)
 export(install_appmamba)
 export(kraken2)

R/cmd-freebayes.R

@@ -0,0 +1,53 @@
+#' Run freebayes
+#'
+#'freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, 
+#'specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), 
+#'MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) 
+#'smaller than the length of a short-read sequencing alignment.
+#' @param ref A string of reference file path.
+#' @param input A string of path to the input bam file.
+#' @param ofile A string of path to the output vcf file.
+#' @param ... `r rd_dots("freebayes")`.
+#' @param freebayes `r rd_cmd("freebayes")`.
+#' @family command
+#' @inherit exec return
+#' @seealso
+#' - <https://github.com/freebayes/freebayes>
+#'
+#' `r rd_seealso()`
+#' @export
+freebayes <- make_command(
+  "freebayes",
+  function(
+    ref,
+    input,
+    ofile,
+    ...,
+    freebayes = NULL
+  ){
+    assert_string(freebayes, allow_empty = FALSE, allow_null = TRUE)
+    Freebayes$new(
+      cmd = freebayes,
+      ...,
+      ref = ref,
+      input = input,
+      ofile = ofile,
+    )
+  }
+)
+
+Freebayes <- R6Class(
+  "Freebayes",
+  inherit = Command,
+  private = list(
+    alias = function() "freebayes",
+    setup_help_params = function() "--help",
+    setup_command_params = function(ref, input, ofile){
+      c(
+        arg0("-f", ref),
+        arg0("-b", input),
+        arg0("-v", ofile)
+      )
+    }
+  )
+)

R/minimap2.R R/cmd-minimap2.RR/minimap2.R renamed to R/cmd-minimap2.R

@@ -54,6 +54,7 @@ reference:
     - gistic2
     - strelka
     - minimap2
+    - freebayes
 
   - title: "Transcriptomic tools"
     desc: "Wrappers for transcriptome sequencing data processing and analysis tools."