Improved message

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -73,8 +73,8 @@ class BamMetrics(val root: Configurable) extends QScript
   /** executed before script */
   def init(): Unit = {
     inputFiles :+= new InputFile(inputBam)
-    ampliconBedFile.foreach(BedCheck.checkBedFileToReference(_, referenceFasta()))
-    roiBedFiles.foreach(BedCheck.checkBedFileToReference(_, referenceFasta()))
+    ampliconBedFile.foreach(BedCheck.checkBedFileToReference(_, referenceFasta(), biopetError = true))
+    roiBedFiles.foreach(BedCheck.checkBedFileToReference(_, referenceFasta(), biopetError = true))
   }
 
   /** Script to add jobs */

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedCheck.scala

@@ -19,7 +19,7 @@ object BedCheck {
         try {
           bedrecords.validateContigs(reference)
         } catch {
-          case e: IllegalArgumentException => Logging.addError(e.getMessage)
+          case e: IllegalArgumentException => Logging.addError(e.getMessage + s", Bedfile: $bedFile")
         }
       } else bedrecords.validateContigs(reference)
     }