Fix bug for #181

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -46,7 +46,7 @@ object ConfigUtils extends Logging {
         map1(key) match {
           case m1: Map[_, _] =>
             map2(key) match {
-              case m2: Map[_, _] => newMap += (key -> mergeMaps(any2map(m1), any2map(m2)))
+              case m2: Map[_, _] => newMap += (key -> mergeMaps(any2map(m1), any2map(m2), resolveConflict))
               case _             => newMap += (key -> map1(key))
             }
           case _ => newMap += (key -> resolveConflict(map1(key), map2(key), key))

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala

@@ -217,7 +217,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
 
   @Test def testNestedMergeConflict: Unit = {
     val map1 = Map("c" -> Map("x" -> "1"))
-    val map2 = Map("c" -> Map("x" -> "1"))
+    val map2 = Map("c" -> Map("x" -> "2"))
     mergeMaps(map1, map2) shouldBe Map("c" -> Map("x" -> "1"))
     mergeMaps(map1, map2, (a, b, k) => a.toString + b.toString) shouldBe Map("c" -> Map("x" -> "12"))
     mergeMaps(map2, map1, (a, b, k) => a.toString + b.toString) shouldBe Map("c" -> Map("x" -> "21"))