Merge branch 'fix-compile_issues' into 'develop'

Fix compile issues



See merge request !352

public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala

@@ -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
 
-
   }
 
 }

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala

@@ -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

public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -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 {