Commit 566bfacd authored by bow's avatar bow
Browse files

Supply default arguments to samtools view wrapper

parent d205c898
...@@ -21,16 +21,16 @@ import java.io.File ...@@ -21,16 +21,16 @@ import java.io.File
class SamtoolsView(val root: Configurable) extends Samtools { class SamtoolsView(val root: Configurable) extends Samtools {
@Input(doc = "Bam File") @Input(doc = "Bam File")
var input: File = _ var input: File = null
@Output(doc = "output File") @Output(doc = "output File")
var output: File = _ var output: File = null
var quality: Option[Int] = config("quality") var quality: Option[Int] = config("quality")
var b: Boolean = config("b") var b: Boolean = config("b", default = false)
var h: Boolean = config("h") var h: Boolean = config("h", default = false)
var f: List[String] = config("f") var f: List[String] = config("f", default = List.empty[String])
var F: List[String] = config("F") var F: List[String] = config("F", default = List.empty[String])
def cmdBase = required(executable) + def cmdBase = required(executable) +
required("view") + required("view") +
......
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