From 9b16ee45bf5a7e2f74619c318b7a4f6f402bda71 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 4 Mar 2015 14:43:26 +0100
Subject: [PATCH] fix executable
---
.../main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
index 0653abf52..72317bb77 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
@@ -4,7 +4,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvan_thof on 3/4/15.
@@ -18,7 +18,10 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
protected var output: File = null
var p: Option[String] = config("p")
- executable = config("exe", default = "bgzip")
+
+ executable = config("exe", default = "tabix")
+ override val versionRegex = """version: (.*)""".r
+ override def versionCommand = executable
override def beforeGraph: Unit = {
output = new File(input.getAbsolutePath + ".tbi")
--
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