From 7439f3d40f64f2bde144db7764640985b1af8fdd Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Nov 2014 09:56:02 +0100
Subject: [PATCH] Fix typo
---
.../sasc/biopet/pipelines/gatk/GatkVariantcalling.scala | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
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 884b2d837..65f5834b5 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
@@ -61,12 +61,12 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
if (files.size == 1) return files
if (files.isEmpty) throw new IllegalStateException("Files can't be empty")
if (!doublePreProces.get) return files
- val markDub = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
- add(markDub, isIntermediate = useIndelRealigner)
+ val markDup = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
+ add(markDup, isIntermediate = useIndelRealigner)
if (useIndelRealigner) {
- List(addIndelRealign(markDub.output, outputDir, isIntermediate = false))
+ List(addIndelRealign(markDup.output, outputDir, isIntermediate = false))
} else {
- List(markDub.output)
+ List(markDup.output)
}
}
--
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