Commit 4ddf34bf authored by sajvanderzeeuw's avatar sajvanderzeeuw
Browse files

Added all BWA mem options

parent c36fb267
......@@ -18,10 +18,36 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
var RG: String = _
var R: String = config("R")
var k: Option[Int] = config("k")
var r: Option[Float] = config("r")
var S: Boolean = config("S")
var M: Boolean = config("M", default = true)
var w: Option[Int] = config("w")
var d: Option[Int] = config("d")
var c: Option[Int] = config("c")
var D: Option[Float] = config("D")
var W: Option[Int] = config("W")
var m: Option[Int] = config("m")
var P: Boolean = config("P")
var e: Boolean = config("e")
var A: Option[Int] = config("A")
var B: Option[Int] = config("B")
var O: String = config("O")
var E: String = config("E")
var L: String = config("L")
var U: Option[Int] = config("U")
var x: String = config("x")
var p: Boolean = config("p")
var v: Option[Int] = config("v")
var T: Option[Int] = config("T")
var h: Option[Int] = config("h")
var a: Boolean = config("a")
var C: Boolean = config("C")
var Y: Boolean = config("Y")
var I: String = config("I")
executable = config("exe", default = "bwa")
executable = config("exe", default = "bwa", freeVar = false)
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0, 1)
......@@ -33,9 +59,12 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
def cmdLine = {
required(executable) +
required("mem") +
optional("-k", k) +
optional("-r", r) +
optional("-t", nCoresRequest) +
optional("-R", RG) +
optional("-R", R) +
conditional(M, "-M") +
conditional(S, "-S") +
required(reference) +
required(R1) +
optional(R2) +
......
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