Commit ede07209 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'fix-compile_issues' into 'develop'

Fix compile issues



See merge request !352
parents f3779b52 e6d50ed6
......@@ -8,11 +8,10 @@ import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
/**
* Created by ahbbollen on 3-3-16.
*/
* Created by ahbbollen on 3-3-16.
*/
class VariantEffectPredictorTest extends TestNGSuite with Matchers {
@Test
def testSummaryStats = {
val file = new File(Paths.get(getClass.getResource("/vep.metrics").toURI).toString)
......@@ -31,7 +30,6 @@ class VariantEffectPredictorTest extends TestNGSuite with Matchers {
stats.contains("Distribution_of_variants_on_chromosome_1") shouldBe true
stats.contains("Position_in_protein") shouldBe true
}
}
......@@ -130,7 +130,7 @@ object SeqStat extends ToolCommand {
baseStats ++= mutable.ArrayBuffer.fill(record.length - baseStats.length)(BaseStat())
}
if (readStats.lengths.length <= record.length) {
if (readStats.lengths.length <= record.length)
readStats.lengths ++= mutable.ArrayBuffer.fill(record.length - readStats.lengths.length + 1)(0)
val readQuality = record.getBaseQualityString
......
......@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.gentrap
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions._
......@@ -25,7 +25,7 @@ import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{DataProvider, Test}
import org.testng.annotations.{ DataProvider, Test }
abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNGSuite with Matchers {
......
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