Make sure WipeReads also checks for single reads when filtering + writing

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala

@@ -328,6 +328,8 @@ object WipeReads extends MainCommand {
         case rec: SAMRecord if rec.getReadPairedFlag =>
           filteredOutSet.contains(rec.getReadName + "_" + rec.getAlignmentStart).isTrue &&
           filteredOutSet.contains(rec.getReadName + "_" + rec.getMateAlignmentStart).isTrue
+        case rec: SAMRecord if !rec.getReadPairedFlag =>
+            filteredOutSet.contains(rec.getReadName + "_" + rec.getAlignmentStart).isTrue
         case rec: String    => filteredOutSet.contains(rec).isTrue
         case _              => false
       }