From 287bb52e81e12442abd575b90b70129172848683 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 May 2009 20:36:12 +0000
Subject: [PATCH] Refreshes the mount points that we'll be using (so that the
 program will play nicely with LSF).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@783 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/secondarybase/AnnotateSecondaryBase.java    | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java b/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
index 31ac2bd17..1a59f263c 100755
--- a/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
+++ b/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
@@ -2,10 +2,7 @@ package org.broadinstitute.sting.secondarybase;
 
 import net.sf.samtools.*;
 import net.sf.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.Pair;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
 
@@ -135,7 +132,11 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
     private File getTempSAMFile(String prefix) {
         try {
             File tempFile = File.createTempFile(prefix, ".sam", SAM_OUT.getParentFile());
-            tempFile.deleteOnExit();
+            //tempFile.deleteOnExit();
+
+            // Ensure that the volumes we're about to use are ready.
+            PathUtils.refreshVolume(tempFile);
+            PathUtils.refreshVolume(new File(System.getProperty("java.io.tmpdir")));
 
             return tempFile;
         } catch (IOException e) {