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kill job argument to BDGSparkCommand #38

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Merged
merged 1 commit into from
May 3, 2015
Merged

kill job argument to BDGSparkCommand #38

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7 changes: 2 additions & 5 deletions utils-cli/src/main/scala/org/bdgenomics/utils/cli/BDGCommand.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,8 @@
package org.bdgenomics.utils.cli

import java.io.{ StringWriter, PrintWriter }
import org.apache.hadoop.mapreduce.Job
import org.apache.spark.{ SparkConf, Logging, SparkContext }
import org.bdgenomics.utils.instrumentation._
import org.bdgenomics.utils.misc.HadoopUtil

trait BDGCommandCompanion {
val commandName: String
Expand All @@ -42,7 +40,7 @@ trait BDGCommand extends Runnable {
trait BDGSparkCommand[A <: Args4jBase] extends BDGCommand with Logging {
protected val args: A

def run(sc: SparkContext, job: Job)
def run(sc: SparkContext)

def run() {
val start = System.nanoTime()
Expand All @@ -51,9 +49,8 @@ trait BDGSparkCommand[A <: Args4jBase] extends BDGCommand with Logging {
conf.setMaster("local[%d]".format(Runtime.getRuntime.availableProcessors()))
}
val sc = new SparkContext(conf)
val job = HadoopUtil.newJob()
val metricsListener = initializeMetrics(sc)
run(sc, job)
run(sc)
val totalTime = System.nanoTime() - start
printMetrics(totalTime, metricsListener)
}
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