Commit cf338a86 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding vt decompose extension

parent ac9315e7
package nl.lumc.sasc.biopet.extensions.vt
import java.io.File
import nl.lumc.sasc.biopet.core.{Reference, Version}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
/**
* Created by pjvanthof on 20/11/15.
*/
class VtDecompose(val root: Configurable) extends Vt with Version with Reference {
def versionRegex = """decompose (.*)""".r
override def versionExitcode = List(0, 1)
def versionCommand = executable + " decompose"
@Input(required = true)
var inputVcf: File = _
@Output(required = true)
var outputVcf: File = _
var intervalsFile: Option[File] = config("intervals_file")
val smartDecompose: Boolean = config("smart_decompose", default = false)
def cmdLine = required(executable) + required("decompose") +
required("-o", outputVcf) +
optional("-I", intervalsFile) +
conditional(smartDecompose, "-s") +
required(inputVcf)
}
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