From 1f4469976e0397122e6ced5fd81f94cfcdf6c1c6 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 12 Jun 2011 03:38:52 +0000
Subject: [PATCH] Made into UserException with better error message

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5977 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/datasources/reads/BAMSchedule.java              | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
index bc6089d1c..34693d501 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
@@ -31,6 +31,7 @@ import net.sf.samtools.GATKChunk;
 import net.sf.samtools.util.CloseableIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.IOException;
@@ -267,7 +268,7 @@ public class BAMSchedule implements CloseableIterator<BAMScheduleEntry> {
             scheduleFileChannel = new RandomAccessFile(scheduleFile,"rw").getChannel();
         }
         catch(IOException ex) {
-            throw new ReviewedStingException("Unable to create BAM schedule file.",ex);
+            throw new UserException("Unable to create a temporary BAM schedule file.  Please make sure Java can write to the default temp directory or use -Djava.io.tmpdir= to instruct it to use a different temp directory instead.",ex);
         }
         scheduleFile.deleteOnExit();