From b43464ed66fe405adb0bb1dd2edad0c4b6b0e0a9 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 6 Apr 2017 16:11:21 +0200
Subject: [PATCH] Give a warning in de logwhen a variantcaller is used that
 does not support this.

---
 .../scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
index fd7e96b77..f856142db 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
@@ -245,6 +245,14 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
       if (!usePrintReads)
         vc.inputBqsrFiles = samples.flatMap { case (sampleId, sample) => sample.bqsrFile.map(sampleId -> _) }
       add(vc)
+      if (!usePrintReads) {
+        import variantcallers._
+        if (vc.callers.exists(_ match {
+          case _:HaplotypeCaller | _:HaplotypeCallerAllele | _:HaplotypeCallerGvcf => false
+          case _:UnifiedGenotyper | _:UnifiedGenotyperAllele => false
+          case _ => true
+        })) logger.warn("Not all variantcallers chosen can read BQSR files, All non-GATK")
+      }
 
       annotation.foreach { toucan =>
         toucan.outputDir = new File(outputDir, "annotation")
-- 
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