Commit 2a789532 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added Queue wrapper

parent 2b4cb228
......@@ -9,11 +9,31 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
import htsjdk.variant.vcf.VCFFileReader
import htsjdk.variant.vcf.VCFHeader
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
import scala.collection.SortedMap
import scala.collection.immutable.SortedSet
import scala.collection.mutable.{ Map, Set }
import nl.lumc.sasc.biopet.core.config.Configurable
import scala.collection.JavaConversions._
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
@Input(doc = "Input vcf files", shortName = "input", required = true)
var input: List[File] = Nil
@Output(doc = "Output fastq files", shortName = "output", required = true)
var output: File = _
@Argument
var reference: File = config("reference")
override def commandLine = super.commandLine +
repeat("-I", input) +
required("-o", output) +
required("-R", reference)
}
object MergeAlleles extends ToolCommand {
case class Args(inputFiles: List[File] = Nil, outputFile: File = null, reference: File = null) extends AbstractArgs
......
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