Warning message for #385

toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -58,9 +58,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
 
   lazy val enableScatter: Boolean = config("enable_scatter", default = {
     val ref = new FastaSequenceFile(referenceFasta(), true)
-    val refLenght = ref.getSequenceDictionary.getReferenceLength
+    val refLength = ref.getSequenceDictionary.getReferenceLength
     ref.close()
-    refLenght > minScatterGenomeSize
+    refLength > minScatterGenomeSize
   })
 
   def sampleInfo: Map[String, Map[String, Any]] = root match {
@@ -92,6 +92,10 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
     } else inputVcf
 
     if (enableScatter) {
+      val doNotRemove: Boolean = config("do_not_remove", namespace = "variant_effect_predictor", default = false)
+      if (doNotRemove) {
+        logger.warn("Chunking combined with do_not_remove possibly leads to mangled CSQ fields")
+      }
       val outputVcfFiles = BedRecordList.fromReference(referenceFasta())
         .scatter(config("bin_size", default = 50000000))
         .allRecords.map { region =>