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add few queue script and the CatVariantsGatherer scala class

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Ami Levy-Moonshine 2012-12-26 13:06:36 -05:00
parent 3ca3fd4b3e
commit fe427cdd77
1 changed files with 29 additions and 0 deletions
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public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala 100644
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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()
}
}