From 2f744f008073e62a1435b373540e2411c65fe86e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 25 Mar 2016 07:56:30 +0100
Subject: [PATCH] Added index as output file
---
.../scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala | 1 +
1 file changed, 1 insertion(+)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
index 0022d15af..2208d0bbf 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
@@ -49,6 +49,7 @@ class GensToVcf(val root: Configurable) extends ToolCommandFunction with Referen
super.beforeGraph()
if (reference == null) reference = referenceFasta()
if (contig == null) throw new IllegalStateException
+ if (outputVcf.getName.endsWith(".vcf.gz")) outputFiles :+= new File(outputVcf.getAbsolutePath + ".tbi")
}
override def cmdLine = super.cmdLine +
--
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