From bc3e6582f7ee15f9fd259b46a71ff843a567bd73 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 8 Nov 2014 19:05:16 +0100
Subject: [PATCH] Style fix
---
.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala | 4 ++--
1 file changed, 2 insertions(+), 2 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 572a3a276..96051dc4a 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
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import java.io.File
-import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter , MergeAlleles}
+import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter, MergeAlleles }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.{ AnalyzeCovariates, BaseRecalibrator, GenotypeGVCFs, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper }
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
@@ -135,7 +135,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
mergBuffer += ("9.raw" -> scriptOutput.rawFilterVcfFile)
if (useAllelesOption.get) {
- val mergeAlleles = MergeAlleles(this,mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz.tbi")
+ val mergeAlleles = MergeAlleles(this, mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz.tbi")
add(mergeAlleles, isIntermediate = true)
if (useHaplotypecaller.get) {
--
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