From fb215ab10a3f4693c3dbeba4afbe1a5b9b6e6069 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 5 Feb 2015 15:47:56 +0100
Subject: [PATCH] Fix bug on vmem
---
.../sasc/biopet/core/BiopetCommandLineFunctionTrait.scala | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index a76bd7e3a..4a5b25f7a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -15,13 +15,11 @@
*/
package nl.lumc.sasc.biopet.core
-//import java.io.BufferedInputStream
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QException
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
-//import scala.io.Source
import scala.sys.process.{ Process, ProcessLogger }
import scala.util.matching.Regex
import java.io.FileInputStream
@@ -62,7 +60,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
vmem = config("vmem")
if (vmem.isEmpty && defaultVmem.nonEmpty) vmem = Some(defaultVmem)
}
- if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
+ if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
super.freezeFieldValues()
--
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