Fixed compile issues

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala

@@ -95,7 +95,7 @@ object SummaryToTsv extends ToolCommand {
   def fetchValues(summary: Summary,
                   paths: Map[String, Array[String]],
                   sample: Boolean = false,
-                  lib: Boolean = lib = false): Map[String, Map[String, Option[Any]]] = {
+                  lib: Boolean = false): Map[String, Map[String, Option[Any]]] = {
     for ((name, path) <- paths)
       yield
         name -> {

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

@@ -101,14 +101,14 @@ object VcfWithVcf extends ToolCommand {
     val header = reader.getFileHeader
     val vcfDict = header.getSequenceDictionary match {
       case r if r != null =>
-        r.assertSameDictionary(referenceDict, ignoreOrder = true)
+        r.assertSameDictionary(referenceDict, true)
         r
       case _ => referenceDict
     }
     val secondHeader = secondaryReader.getFileHeader
 
     secondHeader.getSequenceDictionary match {
-      case r if r != null => r.assertSameDictionary(referenceDict, ignoreOrder = true)
+      case r if r != null => r.assertSameDictionary(referenceDict, true)
       case _ =>
     }
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala

@@ -95,7 +95,7 @@ object BamStats extends ToolCommand {
     referenceFasta
       .map { f =>
         samHeader.getSequenceDictionary.assertSameDictionary(FastaUtils.getCachedDict(f),
-                                                             ignoreOrder = false)
+                                                             false)
         FastaUtils.getCachedDict(f)
       }
       .getOrElse(samHeader.getSequenceDictionary)