From b00a8f2f3a965f00b60a050f776c85c456a9e4f9 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 27 Oct 2015 15:31:19 +0100
Subject: [PATCH] Removed double index
---
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala | 5 -----
1 file changed, 5 deletions(-)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index c896c849e..e9f73da3a 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -274,11 +274,6 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics)
- val oldIndex: File = new File(bam.getAbsolutePath.stripSuffix(".bam") + ".bai")
- val newIndex: File = new File(bam + ".bai")
- val baiLn = Ln(qscript, oldIndex, newIndex)
- add(baiLn)
-
variantcalling.foreach(vc => {
vc.sampleId = Some(sampleId)
vc.outputDir = new File(sampleDir, "variantcalling")
--
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