From c7dbf66d41744cb439b57764510c1a5546ca8902 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Dec 2010 22:38:06 +0000
Subject: [PATCH] Added a javaMemoryLimit option for cases where the java -Xmx
 memory should be lower than the bsub memory limit.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4778 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../queue/function/JavaCommandLineFunction.scala   | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
index 740679414..ebac3465c 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
@@ -9,8 +9,20 @@ trait JavaCommandLineFunction extends CommandLineFunction {
    */
   def javaExecutable: String
 
+  /**
+   * Memory limit for the java executable, or if None will use the default memoryLimit.
+   */
+  var javaMemoryLimit: Option[Int] = None
+
+  override def freezeFieldValues = {
+    super.freezeFieldValues
+
+    if (javaMemoryLimit.isEmpty && memoryLimit.isDefined)
+      javaMemoryLimit = memoryLimit
+  }
+
   def javaOpts = "%s -Djava.io.tmpdir=%s"
-    .format(optional(" -Xmx", memoryLimit, "g"), jobTempDir)
+    .format(optional(" -Xmx", javaMemoryLimit, "g"), jobTempDir)
 
   def commandLine = "java%s %s"
     .format(javaOpts, javaExecutable)