added logging about the parameter ''mate_inner_dist'

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

@@ -281,6 +281,9 @@ class Tophat(val parent: Configurable)
                .filter(_.startsWith(new File(bowtieIndex).getName))
                .exists(_.endsWith(".bt2")))
       throw new IllegalArgumentException("No bowtie2 index found for tophat")
+    if (R2.nonEmpty && mateInnerDist.isEmpty) {
+      logger.warn("The parameter 'mate_inner_dist' is not set in the configuration, TopHat will use it's default value - 50bp, please check if this value for inner mate distance is correct for the current data.")
+    }
   }
 
   def cmdLine: String =