From 41a8a304a0ffc2b6a6209b8da6b4423d8c91bd22 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 7 Sep 2012 11:27:00 -0400
Subject: [PATCH] Catch masked OutOfMemory errors as User Errors

---
 .../src/org/broadinstitute/sting/gatk/CommandLineGATK.java    | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index ce57d1a7a..1b41b85f4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -137,6 +137,10 @@ public class CommandLineGATK extends CommandLineExecutable {
             exitSystemWithUserError(new UserException.NoSpaceOnDevice());
         if ( t.getCause() != null && t.getCause().getMessage().contains("No space left on device") )
             exitSystemWithUserError(new UserException.NoSpaceOnDevice());
+
+        // masked out of memory error
+        if ( t.getCause() != null && t.getCause() instanceof OutOfMemoryError )
+            exitSystemWithUserError(new UserException.NotEnoughMemory());
     }
 
     /**