From 2c1fb614eafe12ba7f4e4e3da339ba04e3b463ab Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Mon, 26 Sep 2016 11:59:37 +0200
Subject: [PATCH] Warning message for #385

---
 .../nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala     | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
index 442c66f29..50bd70e20 100644
--- a/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+++ b/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 =>
-- 
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