testing different output modes

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

@@ -147,10 +147,12 @@ object VcfFilter extends ToolCommand {
       build)
     writer.writeHeader(header)
 
-    val invertedWriter = commandArgs.invertedOutputVcf.collect { case x => new VariantContextWriterBuilder().
-      setOutputFile(x).
-      setReferenceDictionary(header.getSequenceDictionary).
-      build }
+    val invertedWriter = commandArgs.invertedOutputVcf.collect {
+      case x => new VariantContextWriterBuilder().
+        setOutputFile(x).
+        setReferenceDictionary(header.getSequenceDictionary).
+        build
+    }
     invertedWriter.foreach(_.writeHeader(header))
 
     var counterTotal = 0

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

@@ -70,7 +70,6 @@ object VcfWithVcf extends ToolCommand {
       header.addMetaDataLine(newHeaderLine)
     }
 
-
     var idx = 0
 
     for (record <- reader) {

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

@@ -90,10 +90,9 @@ object VepNormalizer extends ToolCommand {
     logger.debug("Parsing header")
     val new_infos = parseCsq(header)
     header.setWriteCommandLine(true)
-
     val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().
       setOutputFile(output).setReferenceDictionary(header.getSequenceDictionary)
-      build())
+      build ())
 
     for (info <- new_infos) {
       val tmpheaderline = new VCFInfoHeaderLine(info, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "A VEP annotation")

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

@@ -15,6 +15,7 @@
  */
 package nl.lumc.sasc.biopet.tools
 
+import scala.util.Random
 import org.scalatest.testng.TestNGSuite
 import org.scalatest.mock.MockitoSugar
 import org.scalatest.Matchers
@@ -41,6 +42,46 @@ class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
   val vepped = new File(resourcePath("/VEP_oneline.vcf"))
   val unvepped = new File(resourcePath("/unvepped.vcf"))
 
+  val vepped_path = resourcePath("/VEP_oneline.vcf")
+
+  val rand = new Random()
+
+  @Test def testGzOutputExplode(): Unit = {
+    val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf.gz"
+    val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
+    main(arguments)
+  }
+
+  @Test def testVcfOutputExplode(): Unit = {
+    val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf"
+    val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
+    main(arguments)
+  }
+
+  @Test def testBcfOutputExplode(): Unit = {
+    val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".bcf"
+    val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
+    main(arguments)
+  }
+
+  @Test def testGzOutputStandard(): Unit = {
+    val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf.gz"
+    val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
+    main(arguments)
+  }
+
+  @Test def testVcfOutputStandard(): Unit = {
+    val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf"
+    val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
+    main(arguments)
+  }
+
+  @Test def testBcfOutputStandard(): Unit = {
+    val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".bcf"
+    val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
+    main(arguments)
+  }
+
   @Test def testVEPHeaderLength() = {
     val reader = new VCFFileReader(vepped, false)
     val header = reader.getFileHeader