diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 516ea8451..bc37b0557 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -63,6 +63,7 @@ import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
 import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor;
 
 import java.io.File;
+import java.io.OutputStream;
 import java.util.*;
 
 /**
@@ -731,6 +732,21 @@ public class GenomeAnalysisEngine {
         outputs.add(stub);
     }
 
+    /**
+     * Iterates over all registered output stubs and tries to find the one representing the given OutputStream.
+     *
+     * @param output  the stream to check for
+     * @return the file associated with the given stream/stub if available, null otherwise
+     */
+    public File getFilenameFromAssociatedOutputStream(final OutputStream output) {
+        for ( final Stub<?> stub : outputs ) {
+            if ( stub.getOutputStream() == output )
+                return stub.getOutputFile();
+        }
+
+        return null;
+    }
+
     /**
      * Returns the tag associated with a given command-line argument.
      * @param key Object for which to inspect the tag.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
index 300e801e6..9f69a4144 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -50,7 +50,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
     private static Logger logger = Logger.getLogger(SAMFileWriterStorage.class);
 
     public SAMFileWriterStorage( SAMFileWriterStub stub ) {
-        this(stub,stub.getSAMFile());   
+        this(stub,stub.getOutputFile());
     }
 
     public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) {
@@ -66,7 +66,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
         if(stub.getMaxRecordsInRam() != null)
             factory.setMaxRecordsInRam(stub.getMaxRecordsInRam());
 
-        if(stub.getSAMFile() != null) {
+        if(stub.getOutputFile() != null) {
             try {
                 this.writer = createBAMWriter(factory,stub.getFileHeader(),stub.isPresorted(),file,stub.getCompressionLevel());
             }
@@ -74,8 +74,8 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
                 throw new UserException.CouldNotCreateOutputFile(file,"file could not be created",ex);
             }
         }
-        else if(stub.getSAMOutputStream() != null){
-            this.writer = factory.makeSAMWriter( stub.getFileHeader(), stub.isPresorted(), stub.getSAMOutputStream());
+        else if(stub.getOutputStream() != null){
+            this.writer = factory.makeSAMWriter( stub.getFileHeader(), stub.isPresorted(), stub.getOutputStream());
         }
         else
             throw new UserException("Unable to write to SAM file; neither a target file nor a stream has been specified");
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 0f5290db7..28ea69f4c 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
@@ -69,9 +69,9 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
      * @param stub Stub to use when constructing the output file.
      */
     public VariantContextWriterStorage(VariantContextWriterStub stub)  {
-        if ( stub.getFile() != null ) {
-            this.file = stub.getFile();
-            writer = vcfWriterToFile(stub,stub.getFile(),true);
+        if ( stub.getOutputFile() != null ) {
+            this.file = stub.getOutputFile();
+            writer = vcfWriterToFile(stub,stub.getOutputFile(),true);
         }
         else if ( stub.getOutputStream() != null ) {
             this.file = null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
index d2e7066e9..633fd0e37 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
@@ -150,7 +150,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      * Retrieves the SAM file to (ultimately) be created.
      * @return The SAM file.  Must not be null.
      */
-    public File getSAMFile() {
+    public File getOutputFile() {
         return samFile;
     }
 
@@ -162,7 +162,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
         simplifyBAM = v;
     }
 
-    public OutputStream getSAMOutputStream() {
+    public OutputStream getOutputStream() {
         return samOutputStream;
     }
 
@@ -220,7 +220,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
 
     /**
      * Gets whether to generate an md5 on-the-fly for this BAM.
-     * @return True generates the md5.  False means skip writing the file.
+     * @param generateMD5   True generates the md5.  False means skip writing the file.
      */
     public void setGenerateMD5(boolean generateMD5) {
         if(writeStarted)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/Stub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/Stub.java
index b042144b6..873f5b7c8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/Stub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/Stub.java
@@ -27,6 +27,9 @@ package org.broadinstitute.sting.gatk.io.stubs;
 
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 
+import java.io.File;
+import java.io.OutputStream;
+
 /**
  * A stub used for managing IO. Acts as a proxy for IO streams
  * not yet created or streams that need significant external
@@ -43,4 +46,14 @@ public interface Stub<StreamType> {
      * @param outputTracker The connector used to provide an appropriate stream.
      */
     public void register( OutputTracker outputTracker );
+
+    /**
+     * Returns the OutputStream represented by this stub or null if not available.
+     */
+    public OutputStream getOutputStream();
+
+    /**
+     * Returns the File represented by this stub or null if not available.
+     */
+    public File getOutputFile();
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
index ee1dc63e6..f92d78bb5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
@@ -140,7 +140,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
      * Retrieves the file to (ultimately) be created.
      * @return The file.  Can be null if genotypeStream is not.
      */
-    public File getFile() {
+    public File getOutputFile() {
         return genotypeFile;
     }
 
@@ -148,7 +148,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
      * Retrieves the output stearm to which to (ultimately) write.
      * @return The file.  Can be null if genotypeFile is not.
      */
-    public PrintStream getOutputStream() {
+    public OutputStream getOutputStream() {
         return genotypeStream;
     }
 
@@ -196,7 +196,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
         if ( engine.lenientVCFProcessing() ) options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
         if ( indexOnTheFly && ! isCompressed() ) options.add(Options.INDEX_ON_THE_FLY);
 
-        if ( forceBCF || (getFile() != null && VariantContextWriterFactory.isBCFOutput(getFile())) )
+        if ( forceBCF || (getOutputFile() != null && VariantContextWriterFactory.isBCFOutput(getOutputFile())) )
             options.add(Options.FORCE_BCF);
 
         return options.isEmpty() ? EnumSet.noneOf(Options.class) : EnumSet.copyOf(options);
@@ -271,7 +271,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
     public boolean alsoWriteBCFForTest() {
         return engine.getArguments().numberOfDataThreads == 1 && // only works single threaded
                 ! isCompressed() && // for non-compressed outputs
-                getFile() != null && // that are going to disk
+                getOutputFile() != null && // that are going to disk
                 engine.getArguments().generateShadowBCF; // and we actually want to do it
     }