From 9dc694b2e9fe4a476636d751297d2bed26e783df Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 16 Aug 2012 10:01:10 -0400
Subject: [PATCH] Meaningful error message and keeping tmp file when mergeInfo
 fails

-- BCF2 is failing for some reason when merging tmp. files with parallel combine variants.  ThreadLocalOutputTracker no longer sets deleteOnExit on the tmp file, as this prevents debugging.  And it's unnecessary because each mergeInto was deleting files as appropriate
-- MergeInfo in VariantContextWriterStorage only deletes the intermediate output if an error occurs
---
 .../broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java | 2 +-
 .../sting/gatk/io/storage/VariantContextWriterStorage.java     | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
index 999deddd1..636787c69 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
@@ -119,7 +119,7 @@ public class ThreadLocalOutputTracker extends OutputTracker {
 
         try {
             tempFile = File.createTempFile( stub.getClass().getName(), null );
-            tempFile.deleteOnExit();
+            //tempFile.deleteOnExit();
         }
         catch( IOException ex ) {
             throw new UserException.BadTmpDir("Unable to create temporary file for stub: " + stub.getClass().getName() );
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
index 161179f84..72f8581dd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
@@ -194,6 +194,9 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
             }
 
             source.close();
+            file.delete(); // this should be last to aid in debugging when the process fails
+        } catch (UserException e) {
+            throw new ReviewedStingException("BUG: intermediate file " + file + " is malformed, got error while reading", e);
         } catch (IOException e) {
             throw new UserException.CouldNotReadInputFile(file, "Error reading file in VCFWriterStorage: ", e);
         }