From 7087956f771ce649ec88e683cb0068ae17732a55 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 21 Mar 2016 18:23:46 +0100
Subject: [PATCH] Fixed extension
---
.../nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
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 4cb4548a0..0022d15af 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
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
*
*/
class GensToVcf(val root: Configurable) extends ToolCommandFunction with Reference {
- def toolObject = nl.lumc.sasc.biopet.tools.BaseCounter
+ def toolObject = nl.lumc.sasc.biopet.tools.GensToVcf
@Input(doc = "Input genotypes file", required = true)
var inputGens: File = _
@@ -56,7 +56,7 @@ class GensToVcf(val root: Configurable) extends ToolCommandFunction with Referen
required("--inputInfo", inputInfo) +
required("--outputVcf", outputVcf) +
optional("--contig", contig) +
- required("--reference", reference) +
+ required("--referenceFasta", reference) +
required("--samplesFile", samplesFile)
}
--
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