Code style fixes

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

@@ -3,9 +3,9 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 import java.util
 
-import htsjdk.samtools.reference.{ FastaSequenceFile, ReferenceSequenceFileFactory }
+import htsjdk.samtools.reference.FastaSequenceFile
 import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, Options, VariantContextWriterBuilder }
-import htsjdk.variant.variantcontext.{ Allele, GenotypeBuilder, VariantContextBuilder }
+import htsjdk.variant.variantcontext.{ Allele, VariantContextBuilder }
 import htsjdk.variant.vcf._
 import nl.lumc.sasc.biopet.utils.ToolCommand
 

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GensToVcfTest.scala

@@ -8,11 +8,11 @@ import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
 /**
-  * Created by pjvan_thof on 4/11/16.
-  */
+ * Created by pjvan_thof on 4/11/16.
+ */
 class GensToVcfTest extends TestNGSuite with Matchers {
   @Test
-  def testGensOnly: Unit = {
+  def testGensOnly(): Unit = {
     val output = File.createTempFile("test.", ".vcf.gz")
     output.deleteOnExit()
     GensToVcf.main(Array(
@@ -25,7 +25,7 @@ class GensToVcfTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testGensInfo: Unit = {
+  def testGensInfo(): Unit = {
     val output = File.createTempFile("test.", ".vcf")
     output.deleteOnExit()
     GensToVcf.main(Array(

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SnptestToVcfTest.scala

@@ -8,11 +8,11 @@ import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
 /**
-  * Created by pjvan_thof on 4/11/16.
-  */
+ * Created by pjvan_thof on 4/11/16.
+ */
 class SnptestToVcfTest extends TestNGSuite with Matchers {
   @Test
-  def testSnptest: Unit = {
+  def testSnptest(): Unit = {
     val output = File.createTempFile("test.", ".vcf.gz")
     output.deleteOnExit()
     SnptestToVcf.main(Array(
@@ -24,7 +24,7 @@ class SnptestToVcfTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testEmptySnptest: Unit = {
+  def testEmptySnptest(): Unit = {
     val output = File.createTempFile("test.", ".vcf.gz")
     output.deleteOnExit()
     SnptestToVcf.main(Array(

public/gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala

@@ -11,8 +11,8 @@ import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
 /**
-  * Created by pjvan_thof on 4/11/16.
-  */
+ * Created by pjvan_thof on 4/11/16.
+ */
 class GwasTestTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): GwasTest = {
     new GwasTest {
@@ -60,7 +60,6 @@ class GwasTestTest extends TestNGSuite with Matchers {
     pipeline.script()
   }
 
-
   @Test
   def testEmpty: Unit = {
     val pipeline = initPipeline(GwasTestTest.config)