From 55aba94557863d05d861952b9208a8d628963c2b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 29 Oct 2015 12:01:42 +0100
Subject: [PATCH] Fixed link to bai file
---
.../scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
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 212bdc29e..2b13c8d41 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
@@ -190,7 +190,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
} else {
val oldBamFile: File = inputBam.get
val oldIndex: File = new File(oldBamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
- val newIndex: File = new File(libDir, oldBamFile.getName.stripSuffix(".bam") + ".bai")
+ val newIndex: File = new File(libDir, bamFile.get.getName.stripSuffix(".bam") + ".bai")
val baiLn = Ln(qscript, oldIndex, newIndex)
add(baiLn)
--
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