From b457ed225d5e717f6e9ee1b5b40805b81046e414 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 8 Nov 2014 19:57:11 +0100
Subject: [PATCH] Added index file as output file
---
.../scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index 8a4140d1c..454f9a41f 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -26,11 +26,20 @@ class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction
@Output(doc = "Output vcf file", shortName = "output", required = true)
var output: File = _
+ @Output(doc = "Output vcf file index", shortName = "output", required = true)
+ private var outputIndex: File = _
+
var reference: File = config("reference")
override val defaultVmem = "8G"
memoryLimit = Option(4)
+ override def afterGraph {
+ super.afterGraph
+ if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
+ if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
+ }
+
override def commandLine = super.commandLine +
repeat("-I", input) +
required("-o", output) +
--
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