diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala new file mode 100644 index 000000000..0a89a4227 --- /dev/null +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala @@ -0,0 +1,29 @@ +package org.broadinstitute.sting.queue.extensions.gatk + +import org.broadinstitute.sting.queue.function.{RetryMemoryLimit, JavaCommandLineFunction} +import org.broadinstitute.sting.queue.function.scattergather.GatherFunction +import org.broadinstitute.sting.queue.util.ClassFieldCache +import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor + +/** + * Created with IntelliJ IDEA. + * User: ami + * Date: 12/11/12 + * Time: 2:04 PM + * To change this template use File | Settings | File Templates. + */ +class CatVariantsGatherer extends CatVariants with GatherFunction with RetryMemoryLimit{ + this.assumeSorted = true + + private lazy val originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK] + + override def freezeFieldValues() { + this.reference = originalGATK.reference_sequence + this.variant = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input"+index) } + this.outputFile = this.originalOutput + super.freezeFieldValues() + } + + + +}