<commit_before>package org.bdgenomics.guacamole.callers

import org.bdgenomics.guacamole.TestUtil.SparkFunSuite
import org.bdgenomics.guacamole.TestUtil
import org.apache.commons.io.FileUtils
import java.io.{ IOError, File }

class SomaticThresholdVariantCallerSuite extends SparkFunSuite {
  sparkTest("run the caller") {
    val output = "/tmp/somatic.threshold.chr20.vcf"
    TestUtil.deleteIfExists(output)
    val caller = SomaticThresholdVariantCaller
    caller.run(Array[String](
      "-tumor-reads", TestUtil.testDataPath("synth1.tumor.100k-200k.withmd.bam"),
      "-normal-reads", TestUtil.testDataPath("synth1.normal.100k-200k.withmd.bam"),
      "-parallelism", "20",
      "-out", output))
  }
}<commit_msg>remove unnecessary / redundant sparkTest() call<commit_after>package org.bdgenomics.guacamole.callers

import org.bdgenomics.guacamole.TestUtil.SparkFunSuite
import org.bdgenomics.guacamole.TestUtil
import org.apache.commons.io.FileUtils
import java.io.{ IOError, File }

class SomaticThresholdVariantCallerSuite extends SparkFunSuite {
  val output = "/tmp/somatic.threshold.chr20.vcf"
  TestUtil.deleteIfExists(output)
  val caller = SomaticThresholdVariantCaller
  caller.run(
    Array[String](
      "-tumor-reads", TestUtil.testDataPath("synth1.tumor.100k-200k.withmd.bam"),
      "-normal-reads", TestUtil.testDataPath("synth1.normal.100k-200k.withmd.bam"),
      "-parallelism", "20",
      "-out", output
    )
  )
}
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