From 8552aa61dd450fda54837b5ac53f5288039fe041 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Nov 2014 09:06:22 +0100
Subject: [PATCH] fix on no known sites warning
---
.../nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index b4f8c127c..884b2d837 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -51,7 +51,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
else if (!outputDir.endsWith("/")) outputDir += "/"
val baseRecalibrator = new BaseRecalibrator(this)
- if (useBaseRecalibration && baseRecalibrator.knownSites.isEmpty) {
+ if (preProcesBams && useBaseRecalibration && baseRecalibrator.knownSites.isEmpty) {
logger.warn("No Known site found, skipping base recalibration")
useBaseRecalibration = false
}
--
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