From fb2fc6954cf90bbfd14573bd94911f840f5c812d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Aug 2015 13:45:52 +0200
Subject: [PATCH] Fix output file
---
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
index ab60204ac..a53409bee 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
@@ -71,7 +71,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
super.beforeGraph()
if (reference == null) reference = referenceFasta()
if (outFileNamePrefix != null && !outFileNamePrefix.endsWith(".")) outFileNamePrefix += "."
- val prefix = if (outFileNamePrefix != null) outputDir + outFileNamePrefix else outputDir
+ val prefix = if (outFileNamePrefix != null) outputDir + File.separator + outFileNamePrefix else outputDir
if (runmode == null) {
outputSam = new File(prefix + "Aligned.out.sam")
outputTab = new File(prefix + "SJ.out.tab")
--
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