Skip empty values

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

@@ -301,9 +301,10 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
 
     (for ((header, headerIndex) <- headers) yield {
       val name = header.stripPrefix("[").stripSuffix("]")
-      name.replaceAll(" ", "_") -> (contents.drop(headerIndex + 1).takeWhile(!isHeader(_)).map { line =>
+      name.replaceAll(" ", "_") -> (contents.drop(headerIndex + 1).takeWhile(!isHeader(_)).flatMap { line =>
         val values = line.split("\t", 2)
-        values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(values.last)
+        if (values.last.isEmpty || values.last == "-") None
+        else Some(values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(values.last))
       }.toMap)
     }).toMap
   }