Adding check for database and cache. Removing print statements in normalizer test

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

@@ -26,6 +26,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   //Boolean vars
   var v: Boolean = config("v")
   var q: Boolean = config("q")
+  var offline: Boolean = config("offline")
   var no_progress: Boolean = config("no_progress")
   var everything: Boolean = config("everything")
   var force: Boolean = config("force")
@@ -124,12 +125,22 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   var db_version: Option[Int] = config("db_version")
   var buffer_size: Option[Int] = config("buffer_size")
 
+  override def afterGraph: Unit = {
+    super.afterGraph
+    if (!cache && !database) {
+      throw new IllegalArgumentException("Must supply either cache or database")
+    } else if (cache && dir == null) {
+      throw new IllegalArgumentException("Must supply dir to cache")
+    }
+  }
+
   def cmdLine = required(executable) +
     required(vep_script) +
     required("-i", input) +
     required("-o", output) +
     conditional(v, "-v") +
     conditional(q, "-q") +
+    conditional(offline, "--offline") +
     conditional(no_progress, "--no_progress") +
     conditional(everything, "--everything") +
     conditional(force, "--force_overwrite") +

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

@@ -102,7 +102,7 @@ object VEPNormalizer extends ToolCommand {
     val writerBuilder = new VariantContextWriterBuilder()
     writerBuilder.
       setOutputFile(output).
-      setOutputFileType(VariantContextWriterBuilder.OutputType.VCF).
+      setOutputFileType(VariantContextWriterBuilder.OutputType.BLOCK_COMPRESSED_VCF).
       setReferenceDictionary(seqDict)
     val writer = writerBuilder.build()
     writer.writeHeader(header)

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

@@ -56,7 +56,6 @@ class VEPNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
     }
 
     def check(item: String) = {
-      println(record.getAttribute(item))
       record.getAttribute(item).toString.split(""",""", -1).length should be(11)
     }