From 7dbba465ee22d21ff9a2f1fca46963a3092b7d00 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 22 Jun 2012 11:32:18 -0400
Subject: [PATCH] Bugfix for shadow BCFs to not attempt to write to
 /dev/null.bcf

---
 .../gatk/io/storage/VariantContextWriterStorage.java  |  6 ++++--
 .../sting/utils/codecs/bcf2/BCF2Utils.java            | 11 ++++++++---
 2 files changed, 12 insertions(+), 5 deletions(-)

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 d0fdae639..fb05a6b04 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
@@ -107,8 +107,10 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
         // TODO -- remove me when argument generateShadowBCF is removed
         if ( stub.alsoWriteBCFForTest() && ! VariantContextWriterFactory.isBCFOutput(file, options)) {
             final File bcfFile = BCF2Utils.shadowBCF(file);
-            VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, stub.getMasterSequenceDictionary(), options);
-            writer = new TestWriter(writer, bcfWriter);
+            if ( bcfFile != null ) {
+                VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, stub.getMasterSequenceDictionary(), options);
+                writer = new TestWriter(writer, bcfWriter);
+            }
         }
 
         return writer;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
index 2669206fe..51fbd3a7f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
@@ -200,8 +200,11 @@ public final class BCF2Utils {
      * foo.vcf => foo.bcf
      * foo.xxx => foo.xxx.bcf
      *
+     * If the resulting BCF file cannot be written, return null.  Happens
+     * when vcfFile = /dev/null for example
+     *
      * @param vcfFile
-     * @return
+     * @return the BCF
      */
     @Requires("vcfFile != null")
     @Ensures("result != null")
@@ -209,8 +212,10 @@ public final class BCF2Utils {
         final String path = vcfFile.getAbsolutePath();
         if ( path.contains(".vcf") )
             return new File(path.replace(".vcf", ".bcf"));
-        else
-            return new File( path + ".bcf" );
+        else {
+            final File bcf = new File( path + ".bcf" );
+            return bcf.canWrite() ? bcf : null;
+        }
     }
 
     @Ensures("BCF2Type.INTEGERS.contains(result)")