Write empty file when no records exist

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

@@ -39,8 +39,6 @@ class SnptestToVcf(val root: Configurable) extends ToolCommandFunction with Refe
 
   var contig: String = _
 
-  override def defaultCoreMemory = 6.0
-
   override def beforeGraph(): Unit = {
     super.beforeGraph()
     if (reference == null) reference = referenceFasta()

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

@@ -48,12 +48,27 @@ object SnptestToVcf extends ToolCommand {
 
     infoHeader match {
       case Some(header) => parseLines(header, infoIt, cmdArgs)
-      case _            => logger.info("No header and records found in file")
+      case _            =>
+        writeEmptyVcf(cmdArgs.outputVcf, cmdArgs.referenceFasta)
+        logger.info("No header and records found in file")
     }
 
     logger.info("Done")
   }
 
+  def writeEmptyVcf(outputVcf: File, referenceFasta: File): Unit = {
+    val reference = new FastaSequenceFile(referenceFasta, true)
+    val vcfHeader = new VCFHeader()
+    vcfHeader.setSequenceDictionary(reference.getSequenceDictionary)
+    val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder()
+      .setOutputFile(outputVcf)
+      .setReferenceDictionary(vcfHeader.getSequenceDictionary)
+      .unsetOption(Options.INDEX_ON_THE_FLY)
+      .build)
+    writer.writeHeader(vcfHeader)
+    writer.close()
+  }
+
   def parseLines(header: String, lineIt: Iterator[String], cmdArgs: Args): Unit = {
     val headerKeys = header.split(" ")
     val headerMap = headerKeys.zipWithIndex.toMap