From 7cdaffbe5c04128e78abb2a34f617085c1d7bc5a Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 5 Jan 2011 03:07:11 +0000
Subject: [PATCH] Create tmpdir if it doesn't exist.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4936 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/GenomeAnalysisEngine.java              | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 4bb14e25c..12c893da8 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -196,6 +196,9 @@ public class GenomeAnalysisEngine {
         // our microscheduler, which is in charge of running everything
         MicroScheduler microScheduler = createMicroscheduler();
 
+        // create temp directories as necessary
+        initializeTempDirectory();
+
         // create the output streams                     "
         initializeOutputStreams(microScheduler.getOutputTracker());
 
@@ -473,6 +476,14 @@ public class GenomeAnalysisEngine {
         return walker instanceof ReadWalker;
     }
 
+    /**
+     * Create the temp directory if it doesn't exist.
+     */
+    private void initializeTempDirectory() {
+        File tempDir = new File(System.getProperty("java.io.tmpdir"));
+        tempDir.mkdirs();
+    }
+
     /**
      * Initialize the output streams as specified by the user.
      *