Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4077 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.alignment;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -37,6 +38,7 @@ import net.sf.samtools.*;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
 
 import java.io.File;
+import java.io.PrintStream;
 
 /**
  * Aligns reads to a given reference using Heng Li's BWA aligner, presenting the resulting alignments in SAM or BAM format.
@@ -53,6 +55,9 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
     @Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false)
     private String outputBamFile = null;
 
+    @Output
+    private PrintStream out = null;
+
     @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
     private Integer bamCompression = 5;
 

java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java

@@ -32,9 +32,11 @@ import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import net.sf.samtools.SAMRecord;
 
 import java.util.*;
+import java.io.PrintStream;
 
 /**
  * Counts the number of best alignments as presented by BWA and outputs a histogram of number of placements vs. the
@@ -50,6 +52,9 @@ public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
     @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
     private String prefix = null;
 
+    @Output
+    private PrintStream out = null;    
+
     /**
      * The actual aligner.
      */

java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.commandline;
 
+import org.broadinstitute.sting.gatk.walkers.Multiplexer;
+
 import java.util.*;
 
 /**
@@ -50,8 +52,17 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
      * Create a new argument match, defining its properties later.  Used to create invalid arguments.
      */
     public ArgumentMatch() {
-        this.label = null;
+        this(null,null);
-        this.definition = null;
+    }
+
+    /**
+     * Minimal constructor for transform function.
+     * @param label Label of the argument match.  Must not be null.
+     * @param definition The associated definition, if one exists.  May be null.
+     */
+    private ArgumentMatch(String label,ArgumentDefinition definition) {
+        this.label = label;
+        this.definition = definition;
     }
 
     /**
@@ -64,6 +75,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
         this( label, definition, index, null );
     }
 
+
     private ArgumentMatch( String label, ArgumentDefinition definition, int index, String value ) {
         this.label = label;
         this.definition = definition;
@@ -74,6 +86,26 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
         indices.put(index,values );
     }
 
+    /**
+     * Reformat the given entries with the given multiplexer and key.
+     * TODO: Generify this.
+     * @param multiplexer Multiplexer that controls the transformation process.
+     * @param key Key which specifies the transform.
+     * @return A variant of this ArgumentMatch with all keys transformed.
+     */
+    ArgumentMatch transform(Multiplexer multiplexer, Object key) {
+        SortedMap<Integer,List<String>> newIndices = new TreeMap<Integer,List<String>>();
+        for(Map.Entry<Integer,List<String>> index: indices.entrySet()) {
+            List<String> newEntries = new ArrayList<String>();
+            for(String entry: index.getValue())
+                newEntries.add(multiplexer.transformArgument(key,entry));
+            newIndices.put(index.getKey(),newEntries);
+        }
+        ArgumentMatch newArgumentMatch = new ArgumentMatch(label,definition);
+        newArgumentMatch.indices.putAll(newIndices);
+        return newArgumentMatch;
+    }
+
     /**
      * Return a string representation of the given argument match, for debugging purposes.
      * @return String representation of the match.

java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.commandline;
 
+import org.broadinstitute.sting.gatk.walkers.Multiplexer;
+
 import java.util.*;
 /**
  * Represents a list of potential matches between the arguments defined
@@ -160,6 +162,19 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
         return matches;
     }
 
+    /**
+     * Reformat the given entries with the given multiplexer and key.
+     * TODO: Generify this.
+     * @param multiplexer Multiplexer that controls the transformation process.
+     * @param key Key which specifies the transform.
+     */
+    ArgumentMatches transform(Multiplexer multiplexer, Object key) {
+        ArgumentMatches newArgumentMatches = new ArgumentMatches();
+        for(ArgumentMatch match: argumentMatches.values())
+            newArgumentMatches.mergeInto(match.transform(multiplexer,key));
+        return newArgumentMatches;
+    }
+
     /**
      * Merges the given argument match into the set of existing argument matches.
      * If multiple arguments are present, those arguments will end up grouped.

java/src/org/broadinstitute/sting/commandline/ArgumentSource.java

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.commandline;
 
+import org.broadinstitute.sting.utils.StingException;
+
 import java.lang.reflect.Field;
 import java.util.Arrays;
 import java.util.List;
@@ -67,9 +69,28 @@ public class ArgumentSource {
      * @param field Field containing the argument.  Field must be annotated with 'Input' or 'Output'.
      */
     public ArgumentSource( Field[] parentFields, Field field ) {
+        this(parentFields,field,ArgumentTypeDescriptor.create(field.getType()));
+    }
+
+    /**
+     * Create a new command-line argument target.
+     * @param parentFields Parent fields containing the the field.  Field must be annotated with 'ArgumentCollection'.
+     * @param field Field containing the argument.  Field must be annotated with 'Input' or 'Output'.
+     * @param typeDescriptor custom type descriptor to use when parsing.
+     */
+    private ArgumentSource( Field[] parentFields, Field field, ArgumentTypeDescriptor typeDescriptor) {
         this.parentFields = parentFields;
         this.field = field;
-        this.typeDescriptor = ArgumentTypeDescriptor.create( field.getType() );
+        this.typeDescriptor = typeDescriptor;
+    }
+
+    /**
+     * Somewhat hackish copy constructor to track fields with a custom type descriptor.
+     * TODO: Separate type descriptor from ArgumentSource in general usage.
+     * @param typeDescriptor New type descriptor for the object.
+     */
+    public ArgumentSource copyWithCustomTypeDescriptor(final ArgumentTypeDescriptor typeDescriptor) {
+        return new ArgumentSource(parentFields,field,typeDescriptor);
     }
 
     /**
@@ -111,15 +132,15 @@ public class ArgumentSource {
      * @return True if this descriptor wants to override any default the user specified.  False otherwise.
      */
     public boolean overridesDefault() {
-        return typeDescriptor.overridesDefault();
+        return typeDescriptor.createsTypeDefault(this,field.getType());
     }
 
     /**
      * Provides the default value for the command-line argument.
      * @return Default value to load into the object.
      */
-    public Object getDefault() {
+    public Object createDefault() {
-        return typeDescriptor.getDefault();
+        return typeDescriptor.createTypeDefault(this,field.getType());
     }
 
     /**
@@ -155,6 +176,26 @@ public class ArgumentSource {
         return field.isAnnotationPresent(Hidden.class);
     }
 
+    /**
+     * Is this command-line argument dependent on some primitive argument types?
+     * @return True if this command-line argument depends on other arguments; false otherwise.
+     */
+    public boolean isDependent() {
+        return typeDescriptor instanceof MultiplexArgumentTypeDescriptor;
+    }
+
+    /**
+     * Builds out a new type descriptor for the given dependent argument as a function
+     * of the containing object.
+     * @param containingObject The containing object.
+     * @return An argument type descriptor for the custom derivative field.
+     */
+    public MultiplexArgumentTypeDescriptor createDependentTypeDescriptor(Object containingObject) {
+        if(!isDependent())
+            throw new StingException("Field " + field.getName() + " is independent; no dependent type descriptor can be derived.");
+        return ((MultiplexArgumentTypeDescriptor)typeDescriptor).createCustomTypeDescriptor(this,containingObject);
+    }
+
     /**
      * Gets a string representation of the argument source for debugging.
      * @return String representation of the argument source.

java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java

@@ -26,11 +26,15 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.gatk.walkers.Multiplex;
+import org.broadinstitute.sting.gatk.walkers.Multiplexer;
 import org.apache.log4j.Logger;
 
 import java.lang.annotation.Annotation;
 import java.lang.reflect.*;
 import java.util.*;
+import java.io.OutputStream;
 
 /**
  * An descriptor capable of providing parsers that can parse any type
@@ -52,7 +56,8 @@ public abstract class ArgumentTypeDescriptor {
      * The type of set used must be ordered (but not necessarily sorted).
      */
     private static Set<ArgumentTypeDescriptor> descriptors = new LinkedHashSet<ArgumentTypeDescriptor>( Arrays.asList(new SimpleArgumentTypeDescriptor(),
-                                                                                                                      new CompoundArgumentTypeDescriptor()) );
+                                                                                                                      new CompoundArgumentTypeDescriptor(),
+                                                                                                                      new MultiplexArgumentTypeDescriptor()) );
 
     /**
      * Adds new, user defined descriptors to the head of the descriptor list.
@@ -88,20 +93,18 @@ public abstract class ArgumentTypeDescriptor {
     public abstract boolean supports( Class type );
 
     /**
-     * This argument type descriptor wants to override any default value the user might have specified. 
+     * Returns false if a type-specific default can be employed.
-     * @return True if this descriptor wants to override any default the user specified.  False otherwise.
+     * @param source Source of the command-line argument.
+     * @return True to throw in a type specific default.  False otherwise.
      */
-    public boolean overridesDefault() {
+    public boolean createsTypeDefault(ArgumentSource source,Class type) { return false; }
-        return false;
-    }
 
     /**
-     * Provides the default value for the command-line argument.
+     * Generates a default for the given type.
-     * @return Default value to load into the object.
+     * @param source Source of the command-line argument.
+     * @return A default value for the given type.
      */
-    public Object getDefault() {
+    public Object createTypeDefault(ArgumentSource source,Class type) { throw new UnsupportedOperationException("Unable to create default for type " + getClass()); }
-        throw new UnsupportedOperationException(String.format("Type descriptor %s cannot override default value of command-line argument",this.getClass()));   
-    }
 
     /**
      * Given the given argument source and attributes, synthesize argument definitions for command-line arguments.
@@ -156,15 +159,7 @@ public abstract class ArgumentTypeDescriptor {
      * @throws IllegalArgumentException If more than one parameterized type is found on the field.
      */
     protected Class getCollectionComponentType( Field field ) {
-            // If this is a parameterized collection, find the contained type.  If blow up if more than one type exists.
+        return null;
-            if( field.getGenericType() instanceof ParameterizedType) {
-                ParameterizedType parameterizedType = (ParameterizedType)field.getGenericType();
-                if( parameterizedType.getActualTypeArguments().length > 1 )
-                    throw new IllegalArgumentException("Unable to determine collection type of field: " + field.toString());
-                return (Class)parameterizedType.getActualTypeArguments()[0];
-            }
-            else
-                return String.class;
     }
 
     /**
@@ -323,6 +318,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
 
     }
     
+
     /**
      * A mapping of the primitive types to their associated wrapper classes.  Is there really no way to infer
      * this association available in the JRE?
@@ -413,4 +409,167 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         else
             throw new StingException("Unsupported compound argument type: " + type);
     }
+
+    /**
+     * Return the component type of a field, or String.class if the type cannot be found.
+     * @param field The reflected field to inspect.
+     * @return The parameterized component type, or String.class if the parameterized type could not be found.
+     * @throws IllegalArgumentException If more than one parameterized type is found on the field.
+     */
+    @Override
+    protected Class getCollectionComponentType( Field field ) {
+            // If this is a parameterized collection, find the contained type.  If blow up if more than one type exists.
+            if( field.getGenericType() instanceof ParameterizedType) {
+                ParameterizedType parameterizedType = (ParameterizedType)field.getGenericType();
+                if( parameterizedType.getActualTypeArguments().length > 1 )
+                    throw new IllegalArgumentException("Unable to determine collection type of field: " + field.toString());
+                return (Class)parameterizedType.getActualTypeArguments()[0];
+            }
+            else
+                return String.class;
+    }
+}
+
+class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
+    /**
+     * The multiplexer controlling how data is split.
+     */
+    private final Multiplexer multiplexer;
+
+    /**
+     * The set of identifiers for the multiplexed entries.
+     */
+    private final Collection<?> multiplexedIds;
+
+    public MultiplexArgumentTypeDescriptor() {
+        this.multiplexer = null;
+        this.multiplexedIds = null;
+    }
+
+    /**
+     * Private constructor to use in creating a closure of the MultiplexArgumentTypeDescriptor specific to the
+     * given set of multiplexed ids.
+     * @param multiplexedIds The collection of multiplexed entries
+     */
+    private MultiplexArgumentTypeDescriptor(final Multiplexer multiplexer, final Collection<?> multiplexedIds) {
+        this.multiplexer = multiplexer;
+        this.multiplexedIds = multiplexedIds;
+    }
+
+    @Override
+    public boolean supports( Class type ) {
+        return ( Map.class.isAssignableFrom(type) );
+    }
+
+    @Override
+    public boolean createsTypeDefault(ArgumentSource source,Class type) {
+        if(multiplexer == null || multiplexedIds == null)
+            throw new StingException("No multiplexed ids available");
+        // Always create a multiplexed mapping.
+        return true;
+    }
+
+    @Override
+    public Object createTypeDefault(ArgumentSource source,Class type) {
+        if(multiplexer == null || multiplexedIds == null)
+            throw new StingException("No multiplexed ids available");
+
+        Map<Object,Object> multiplexedMapping = new HashMap<Object,Object>();
+        Class componentType = getCollectionComponentType(source.field);
+        ArgumentTypeDescriptor componentTypeDescriptor = ArgumentTypeDescriptor.create(componentType);
+
+        for(Object id: multiplexedIds) {
+            Object value = null;
+            if(componentTypeDescriptor.createsTypeDefault(source,componentType))
+                value = componentTypeDescriptor.createTypeDefault(source,componentType);
+            multiplexedMapping.put(id,value);
+        }
+        return multiplexedMapping;
+    }
+
+
+    @Override
+    public Object parse( ArgumentSource source, Class type, ArgumentMatches matches ) {
+        if(multiplexedIds == null)
+            throw new StingException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first.");
+
+        Map<Object,Object> multiplexedMapping = new HashMap<Object,Object>();
+        Class componentType = getCollectionComponentType(source.field);
+
+        for(Object id: multiplexedIds) {
+            Object value = ArgumentTypeDescriptor.create(componentType).parse(source,componentType,matches.transform(multiplexer,id));
+            multiplexedMapping.put(id,value);
+        }
+        return multiplexedMapping;
+    }
+
+    public MultiplexArgumentTypeDescriptor createCustomTypeDescriptor(ArgumentSource dependentArgument,Object containingObject) {
+        String[] sourceFields = dependentArgument.field.getAnnotation(Multiplex.class).arguments();
+
+        List<ArgumentSource> allSources = ParsingEngine.extractArgumentSources(containingObject.getClass());
+        Class[] sourceTypes = new Class[sourceFields.length];
+        Object[] sourceValues = new Object[sourceFields.length];
+        int currentField = 0;
+
+        for(String sourceField: sourceFields) {
+            boolean fieldFound = false;
+            for(ArgumentSource source: allSources) {
+                if(!source.field.getName().equals(sourceField))
+                    continue;
+                if(source.field.isAnnotationPresent(Multiplex.class))
+                    throw new StingException("Command-line arguments can only depend on independent fields");
+                sourceTypes[currentField] = source.field.getType();
+                sourceValues[currentField] = JVMUtils.getFieldValue(source.field,containingObject);
+                currentField++;
+                fieldFound = true;
+            }
+            if(!fieldFound)
+                throw new StingException(String.format("Unable to find source field %s, referred to by dependent field %s",sourceField,dependentArgument.field.getName()));
+        }
+
+        Class<? extends Multiplexer> multiplexerType = dependentArgument.field.getAnnotation(Multiplex.class).value();
+        Constructor<? extends Multiplexer> multiplexerConstructor = null;
+        try {
+            multiplexerConstructor = multiplexerType.getConstructor(sourceTypes);
+            multiplexerConstructor.setAccessible(true);
+        }
+        catch(NoSuchMethodException ex) {
+            throw new StingException(String.format("Unable to find constructor for class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+        }
+
+        Multiplexer multiplexer = null;
+        try {
+            multiplexer = multiplexerConstructor.newInstance(sourceValues);
+        }
+        catch(IllegalAccessException ex) {
+            throw new StingException(String.format("Constructor for class %s with parameters %s is inaccessible",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+        }
+        catch(InstantiationException ex) {
+            throw new StingException(String.format("Can't create class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+        }
+        catch(InvocationTargetException ex) {
+            throw new StingException(String.format("Can't invoke constructor of class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+        }
+
+        return new MultiplexArgumentTypeDescriptor(multiplexer,multiplexer.multiplex());
+    }
+
+    /**
+     * Return the component type of a field, or String.class if the type cannot be found.
+     * @param field The reflected field to inspect.
+     * @return The parameterized component type, or String.class if the parameterized type could not be found.
+     * @throws IllegalArgumentException If more than one parameterized type is found on the field.
+     */
+    @Override
+    protected Class getCollectionComponentType( Field field ) {
+        // Multiplex arguments must resolve to maps from which the clp should extract the second type.
+        if( field.getGenericType() instanceof ParameterizedType) {
+            ParameterizedType parameterizedType = (ParameterizedType)field.getGenericType();
+            if( parameterizedType.getActualTypeArguments().length != 2 )
+                throw new IllegalArgumentException("Unable to determine collection type of field: " + field.toString());
+            return (Class)parameterizedType.getActualTypeArguments()[1];
+        }
+        else
+            return String.class;
+    }
 }

java/src/org/broadinstitute/sting/commandline/Output.java

@@ -40,7 +40,7 @@ public @interface Output {
      * prefixed on the command-line with a double dash (--).
      * @return Selected full name, or "" to use the default.
      */
-    String fullName() default "";
+    String fullName() default "out";
 
     /**
      * Specified short name of the command.  Short names should be prefixed
@@ -48,21 +48,21 @@ public @interface Output {
      * short names or be separated from them by a space.
      * @return Selected short name, or "" for none.
      */
-    String shortName() default "";
+    String shortName() default "o";
 
     /**
      * Documentation for the command-line argument.  Should appear when the
      * --help argument is specified.
      * @return Doc string associated with this command-line argument.
      */
-    String doc();
+    String doc() default "An output file presented to the walker.  Will overwrite contents if file exists.";
 
     /**
      * Is this command-line argument required.  The application should exit
      * printing help if this command-line argument is not specified.
      * @return True if the argument is required.  False otherwise.
      */
-    boolean required() default true;
+    boolean required() default false;
 
     /**
      * Should this command-line argument be exclusive of others.  Should be

java/src/org/broadinstitute/sting/commandline/ParsingEngine.java

@@ -254,10 +254,24 @@ public class ParsingEngine {
      */
     public void loadArgumentsIntoObject( Object object ) {
         List<ArgumentSource> argumentSources = extractArgumentSources(object.getClass());
-        for( ArgumentSource argumentSource: argumentSources )
+
+        List<ArgumentSource> dependentArguments = new ArrayList<ArgumentSource>();
+        for( ArgumentSource argumentSource: argumentSources ) {
+            // If this argument source depends on other command-line arguments, skip it and make a note to process it later.
+            if(argumentSource.isDependent()) {
+                dependentArguments.add(argumentSource);
+                continue;
+            }
             loadValueIntoObject( argumentSource, object, argumentMatches.findMatches(argumentSource) );
         }
 
+        for(ArgumentSource dependentArgument: dependentArguments) {
+            MultiplexArgumentTypeDescriptor dependentDescriptor = dependentArgument.createDependentTypeDescriptor(object);
+            ArgumentSource dependentSource = dependentArgument.copyWithCustomTypeDescriptor(dependentDescriptor);
+            loadValueIntoObject(dependentSource,object,argumentMatches.findMatches(dependentSource));
+        }
+    }
+
     /**
      * Loads a single argument into the object and that objects children.
      * @param argumentMatches Argument matches to load into the object.
@@ -277,7 +291,7 @@ public class ParsingEngine {
             throw new StingException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);
 
         for( Object target: targets ) {
-            Object value = (argumentMatches.size() != 0) ? source.parse(argumentMatches) : source.getDefault();
+            Object value = (argumentMatches.size() != 0) ? source.parse(argumentMatches) : source.createDefault();
             JVMUtils.setFieldValue(source.field,target,value);
         }
     }

java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -99,13 +99,9 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      * @return A collection of type descriptors generating implementation-dependent placeholders.
      */
     protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() {
-        return Arrays.asList( new VCFWriterArgumentTypeDescriptor(GATKEngine),
+        return GATKEngine.getArgumentTypeDescriptors();
-                              new SAMFileReaderArgumentTypeDescriptor(GATKEngine),
-                              new SAMFileWriterArgumentTypeDescriptor(GATKEngine),
-                              new OutputStreamArgumentTypeDescriptor(GATKEngine) );
     }
 
-
     /**
      * GATK can add arguments dynamically based on analysis type.
      *

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -44,7 +44,7 @@ import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.filters.ReadGroupBlackListFilter;
 import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.gatk.io.stubs.Stub;
+import org.broadinstitute.sting.gatk.io.stubs.*;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDIntervalGenerator;
@@ -52,6 +52,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.commandline.ArgumentException;
 import org.broadinstitute.sting.commandline.ArgumentSource;
+import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
 
 import java.io.File;
 import java.util.*;
@@ -161,7 +162,7 @@ public class GenomeAnalysisEngine {
         // our microscheduler, which is in charge of running everything
         MicroScheduler microScheduler = createMicroscheduler(my_walker);
 
-        // create the output streams
+        // create the output streams                     "
         initializeOutputStreams(my_walker, microScheduler.getOutputTracker());
 
         initializeIntervals();
@@ -516,6 +517,19 @@ public class GenomeAnalysisEngine {
 
     }
 
+    /**
+     * Subclasses of CommandLinePrograms can provide their own types of command-line arguments.
+     * @return A collection of type descriptors generating implementation-dependent placeholders.
+     */
+    protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() {
+        return Arrays.asList( new VCFWriterArgumentTypeDescriptor(this,System.out),
+                              new SAMFileReaderArgumentTypeDescriptor(this),
+                              new SAMFileWriterArgumentTypeDescriptor(this,System.out),
+                              new OutputStreamArgumentTypeDescriptor(this,System.out) );
+    }
+
+
+
     /**
      * Bundles all the source information about the reads into a unified data structure.
      *
@@ -856,11 +870,6 @@ public class GenomeAnalysisEngine {
      * @param outputTracker the tracker supplying the initialization data.
      */
     private void initializeOutputStreams(Walker walker, OutputTracker outputTracker) {
-        if (argCollection.outErrFileName != null)
-            outputTracker.initializeCoreIO(argCollection.outErrFileName, argCollection.outErrFileName);
-        else
-            outputTracker.initializeCoreIO(argCollection.outFileName, argCollection.errFileName);
-
         for (Map.Entry<ArgumentSource, Object> input : inputs.entrySet())
             outputTracker.addInput(input.getKey(), input.getValue());
         for (Stub<?> stub : outputs)

java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -30,7 +30,6 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.DownsampleType;
 import org.broadinstitute.sting.utils.interval.IntervalSetRule;
 import org.simpleframework.xml.*;
@@ -113,21 +112,6 @@ public class GATKArgumentCollection {
     @Input(fullName = "hapmap_chip", shortName = "hc", doc = "Hapmap chip file", required = false)
     public String HAPMAPChipFile = null;
 
-    /** An output file presented to the walker. */
-    @Element(required = false)
-    @Output(fullName = "out", shortName = "o", doc = "An output file presented to the walker.  Will overwrite contents if file exists.", required = false)
-    public String outFileName = null;
-
-    /** An error output file presented to the walker. */
-    @Element(required = false)
-    @Output(fullName = "err", shortName = "e", doc = "An error output file presented to the walker.  Will overwrite contents if file exists.", required = false)
-    public String errFileName = null;
-
-    /** A joint file for both 'normal' and error output presented to the walker. */
-    @Element(required = false)
-    @Output(fullName = "outerr", shortName = "oe", doc = "A joint file for 'normal' and error output presented to the walker.  Will overwrite contents if file exists.", required = false)
-    public String outErrFileName = null;
-
     @Element(required = false)
     @Argument(fullName = "filterZeroMappingQualityReads", shortName = "fmq0", doc = "If true, mapping quality zero reads will be filtered at the lowest GATK level.  Vastly improves performance at areas with abnormal depth due to mapping Q0 reads", required = false)
     public Boolean filterZeroMappingQualityReads = false;
@@ -325,15 +309,6 @@ public class GATKArgumentCollection {
                 (other.downsampleCoverage != null && !other.downsampleCoverage.equals(this.downsampleCoverage))) {
             return false;
         }
-        if (!other.outFileName.equals(this.outFileName)) {
-            return false;
-        }
-        if (!other.errFileName.equals(this.errFileName)) {
-            return false;
-        }
-        if (!other.outErrFileName.equals(this.outErrFileName)) {
-            return false;
-        }
         if (other.numberOfThreads != this.numberOfThreads) {
             return false;
         }

java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java

@@ -6,13 +6,17 @@ import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.utils.pileup.*;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.*;
+import java.io.PrintStream;
 
 /**
  * Computes the coverage per sample.
  */
 public class CoverageBySample extends LocusWalker<Integer, Integer> {
+    @Output
+    protected PrintStream out;    
 
     private HashSet<String> sampleNames = new HashSet<String>();
 

java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java

@@ -67,30 +67,6 @@ public abstract class OutputTracker {
      */
     protected OutputStreamStub errStub = null;
 
-    /**
-     * Create an object to manage output given filenames for the output and error files.
-     * If no files are specified, returns null.
-     * @param outFileName Name of the output file.
-     * @param errFileName Name of the error file.
-     */
-    public void initializeCoreIO( String outFileName, String errFileName ) {
-        // If the two output streams match and are non-null, initialize them identically.
-        // Otherwise, initialize them separately.
-        if( outFileName != null && outFileName.equals(errFileName) ) {
-            outStub = errStub = new OutputStreamStub(new File(outFileName));
-            addOutput(outStub,new OutputStreamStorage(outStub));
-        }
-        else {
-            outStub = (outFileName != null) ? new OutputStreamStub(new File(outFileName))
-                                            : new OutputStreamStub(System.out);
-            addOutput(outStub,new OutputStreamStorage(outStub));
-
-            errStub = (errFileName != null) ? new OutputStreamStub(new File(errFileName))
-                                            : new OutputStreamStub(System.err);
-            addOutput(errStub,new OutputStreamStorage(errStub));
-        }
-    }
-
     /**
      * Gets the output storage associated with a given stub.
      * @param stub The stub for which to find / create the right output stream.
@@ -100,9 +76,6 @@ public abstract class OutputTracker {
     public abstract <T> T getStorage( Stub<T> stub );
 
     public void prepareWalker( Walker walker ) {
-        installStub( walker, "out", new PrintStream(outStub) );
-        installStub( walker, "err", new PrintStream(errStub) );
-
         for( Map.Entry<ArgumentSource,Object> io: inputs.entrySet() ) {
             ArgumentSource targetField = io.getKey();
             Object targetValue = io.getValue();

java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java

@@ -31,6 +31,7 @@ import net.sf.samtools.util.CloseableIterator;
 import java.io.*;
 
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
+import org.broadinstitute.sting.utils.StingException;
 
 /**
  * Provides temporary storage for SAMFileWriters.
@@ -48,11 +49,18 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
 
     public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) {
         this.file = file;
+        if(stub.getSAMFile() != null) {
             if( stub.getCompressionLevel() != null )
                 this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file, stub.getCompressionLevel() );
             else
                 this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file );
         }
+        else if(stub.getSAMOutputStream() != null){
+            this.writer = new SAMFileWriterFactory().makeSAMWriter( stub.getFileHeader(), stub.isPresorted(), stub.getSAMOutputStream());
+        }
+        else
+            throw new StingException("Unable to write to SAM file; neither a target file nor a stream has been specified");
+    }
 
     public SAMFileHeader getFileHeader() {
         return writer.getFileHeader();

java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java

@@ -4,7 +4,7 @@ import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFHeaderLine;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
@@ -32,7 +32,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
         if(stub.getFile() != null) {
             this.file = stub.getFile();
             try {
-                this.stream = new PrintStream(stub.getFile());
+                this.stream = new PrintStream(file);
             }
             catch(IOException ex) {
                 throw new StingException("Unable to open target output stream",ex);
@@ -45,7 +45,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
         else
             throw new StingException("Unable to create target to which to write; storage was provided with neither a file nor a stream.");
 
-        writer = new VCFWriterImpl(stream);
+        writer = new StandardVCFWriter(stream);
     }
 
     /**
@@ -61,7 +61,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
         catch(IOException ex) {
             throw new StingException("Unable to open target output stream",ex);
         }
-        writer = new VCFWriterImpl(this.stream);
+        writer = new StandardVCFWriter(this.stream);
         Set<String> samples = SampleUtils.getSAMFileSamples(stub.getSAMFileHeader());
         writer.writeHeader(new VCFHeader(null, samples));
     }

java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java

@@ -33,6 +33,7 @@ import java.io.OutputStream;
 import java.io.File;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Field;
 
 /**
  * Insert an OutputStreamStub instead of a full-fledged concrete OutputStream implementations.
@@ -41,14 +42,21 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     /**
      * The engine into which output stubs should be fed.
      */
-    private GenomeAnalysisEngine engine;
+    private final GenomeAnalysisEngine engine;
+
+    /**
+     * The default output stream to write to write this info if
+     */
+    private final OutputStream defaultOutputStream;
 
     /**
      * Create a new OutputStream argument, notifying the given engine when that argument has been created.
      * @param engine Engine to add SAMFileWriter output to.
+     * @param defaultOutputStream Default target for output file.
      */
-    public OutputStreamArgumentTypeDescriptor( GenomeAnalysisEngine engine ) {
+    public OutputStreamArgumentTypeDescriptor(GenomeAnalysisEngine engine,OutputStream defaultOutputStream) {
         this.engine = engine;
+        this.defaultOutputStream = defaultOutputStream;
     }
 
     @Override
@@ -56,6 +64,18 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         return getConstructorForClass(type) != null;
     }
 
+    @Override
+    public boolean createsTypeDefault(ArgumentSource source,Class type) {
+        return true;
+    }
+
+    @Override
+    public Object createTypeDefault(ArgumentSource source,Class type) {
+        OutputStreamStub stub = new OutputStreamStub(defaultOutputStream);
+        engine.addOutput(stub);
+        return createInstanceOfClass(type,stub);        
+    }
+
     @Override
     public Object parse( ArgumentSource source, Class type, ArgumentMatches matches )  {
         ArgumentDefinition definition = createDefaultArgumentDefinition(source);
@@ -65,18 +85,7 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
 
         engine.addOutput(stub);
 
-        try {
+        return createInstanceOfClass(type,stub);
-            return getConstructorForClass(type).newInstance(stub);
-        }
-        catch( InstantiationException ex ) {
-            throw new StingException("Could not instantiate class with OutputStream constructor: " + type.getName());
-        }
-        catch( IllegalAccessException ex ) {
-            throw new StingException("Could not access class with OutputStream constructor: " + type.getName());                        
-        }
-        catch( InvocationTargetException ex ) {
-            throw new StingException("Could not invoke constructor for class with OutputStream constructor: " + type.getName());                        
-        }
     }
 
     /**
@@ -92,4 +101,25 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             return null;
         }
     }
+
+    /**
+     * Creat a new instance of the class accepting a single outputstream constructor.
+     * @param type Type of object to create.
+     * @param outputStream resulting output stream.
+     * @return A new instance of the outputstream-derived class.
+     */
+    private Object createInstanceOfClass(Class type,OutputStream outputStream) {
+        try {
+            return getConstructorForClass(type).newInstance(outputStream);
+        }
+        catch( InstantiationException ex ) {
+            throw new StingException("Could not instantiate class with OutputStream constructor: " + type.getName());
+        }
+        catch( IllegalAccessException ex ) {
+            throw new StingException("Could not access class with OutputStream constructor: " + type.getName());
+        }
+        catch( InvocationTargetException ex ) {
+            throw new StingException("Could not invoke constructor for class with OutputStream constructor: " + type.getName());
+        }
+    }
 }

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010 The Broad Institute
+ * Copyright (c) 2010, The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -12,15 +12,14 @@
  *
  * The above copyright notice and this permission notice shall be
  * included in all copies or substantial portions of the Software.
- *
  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
  * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
  * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
  * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
  * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
  * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ * OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.io.stubs;
@@ -34,6 +33,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import net.sf.samtools.SAMFileReader;
 
 import java.io.File;
+import java.io.OutputStream;
 
 /**
  * Describe how to parse SAMFileReaders.

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java

@@ -35,6 +35,7 @@ import java.lang.annotation.Annotation;
 import java.util.List;
 import java.util.Arrays;
 import java.io.File;
+import java.io.OutputStream;
 
 /**
  * Insert a SAMFileWriterStub  instead of a full-fledged concrete OutputStream implementations.
@@ -49,17 +50,23 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     /**
      * The engine into which output stubs should be fed.
      */
-    private GenomeAnalysisEngine engine;
+    private final GenomeAnalysisEngine engine;
+
+    /**
+     * The default location to which data should be written if the user specifies no such location.
+     */
+    private final OutputStream defaultOutputStream;
 
     /**
      * Create a new SAMFileWriter argument, notifying the given engine when that argument has been created.
      * @param engine Engine to add SAMFileWriter output to.
+     * @param defaultOutputStream the target for the data
      */
-    public SAMFileWriterArgumentTypeDescriptor( GenomeAnalysisEngine engine ) {
+    public SAMFileWriterArgumentTypeDescriptor( GenomeAnalysisEngine engine, OutputStream defaultOutputStream ) {
         this.engine = engine;
+        this.defaultOutputStream = defaultOutputStream;
     }
 
-
     @Override
     public boolean supports( Class type ) {
         return SAMFileWriter.class.equals(type) || StingSAMFileWriter.class.equals(type);
@@ -71,6 +78,18 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
                               createBAMCompressionArgumentDefinition(source) );
     }
 
+    @Override
+    public boolean createsTypeDefault(ArgumentSource source,Class type) {
+        return true;
+    }
+
+    @Override
+    public Object createTypeDefault(ArgumentSource source,Class type) {
+        SAMFileWriterStub stub = new SAMFileWriterStub(engine,defaultOutputStream);
+        engine.addOutput(stub);
+        return stub;
+    }
+
     @Override
     public Object parse( ArgumentSource source, Class type, ArgumentMatches matches )  {
         String writerFileName = getArgumentValue( createBAMArgumentDefinition(source), matches );

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java

@@ -30,6 +30,7 @@ import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
 
 import java.io.File;
+import java.io.OutputStream;
 
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
@@ -59,6 +60,11 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     private final File samFile;
 
+    /**
+     * The target output stream, to be used in place of the SAM file.
+     */
+    private final OutputStream samOutputStream;
+
     /**
      * The validation stringency to apply when reading this file.
      */
@@ -90,6 +96,18 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
     public SAMFileWriterStub( GenomeAnalysisEngine engine, File samFile ) {
         this.engine = engine;
         this.samFile = samFile;
+        this.samOutputStream = null;
+    }
+
+    /**
+     * Create a new stub given the requested SAM file and compression level.
+     * @param engine source of header data, maybe other data about input files.
+     * @param stream Output stream to which data should be written.
+     */
+    public SAMFileWriterStub( GenomeAnalysisEngine engine, OutputStream stream ) {
+        this.engine = engine;
+        this.samFile = null;
+        this.samOutputStream = stream;
     }
 
     /**
@@ -100,6 +118,10 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
         return samFile;
     }
 
+    public OutputStream getSAMOutputStream() {
+        return samOutputStream;
+    }
+
     /**
      * Retrieves the header to use when creating the new SAM file.
      * @return header to use when creating the new SAM file.

java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java

@@ -30,6 +30,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 import java.io.File;
+import java.io.OutputStream;
 import java.lang.annotation.Annotation;
 import java.util.List;
 import java.util.Arrays;
@@ -46,12 +47,19 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
      */
     private GenomeAnalysisEngine engine;
 
+    /**
+      * The default location to which data should be written if the user specifies no such location.
+      */
+    private final OutputStream defaultOutputStream;
+
     /**
      * Create a new GenotypeWriter argument, notifying the given engine when that argument has been created.
      * @param engine the engine to be notified.
+     * @param defaultOutputStream the default output stream to be written to if nothing else is specified.
      */
-    public VCFWriterArgumentTypeDescriptor(GenomeAnalysisEngine engine) {
+    public VCFWriterArgumentTypeDescriptor(GenomeAnalysisEngine engine, OutputStream defaultOutputStream) {
         this.engine = engine;
+        this.defaultOutputStream = defaultOutputStream;
     }
 
     /**
@@ -64,12 +72,6 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         return VCFWriter.class.equals(type);
     }
 
-    /**
-     * Create the argument definitions associated with this source.
-     * Assumes that this type descriptor is relevant for this source.
-     * @param source Source class and field for the given argument.
-     * @return A list of all associated argument definitions.
-     */
     @Override
     public List<ArgumentDefinition> createArgumentDefinitions( ArgumentSource source ) {
         return Arrays.asList( createGenotypeFileArgumentDefinition(source) );
@@ -80,19 +82,15 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
      * @return true always.
      */
     @Override
-    public boolean overridesDefault() {
+    public boolean createsTypeDefault(ArgumentSource source,Class type) {
         return true;
     }
 
-    /**
-     * Provide the default value for this argument.
-     * @return A VCFGenotypeWriter which writes to the default output stream.
-     */
     @Override
-    public Object getDefault() {
+    public Object createTypeDefault(ArgumentSource source,Class type) {
-        VCFWriterStub defaultGenotypeWriter = new VCFWriterStub(engine,System.out);
+        VCFWriterStub stub = new VCFWriterStub(engine,defaultOutputStream);
-        engine.addOutput(defaultGenotypeWriter);
+        engine.addOutput(stub);
-        return defaultGenotypeWriter;       
+        return stub;
     }
 
     /**

java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.io.stubs;
 
 import java.io.File;
 import java.io.PrintStream;
+import java.io.OutputStream;
 
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFHeader;
@@ -83,10 +84,10 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
      * @param engine        GATK engine.
      * @param genotypeStream  stream to (ultimately) write.
      */
-    public VCFWriterStub(GenomeAnalysisEngine engine,PrintStream genotypeStream) {
+    public VCFWriterStub(GenomeAnalysisEngine engine, OutputStream genotypeStream) {
         this.engine = engine;
         this.genotypeFile = null;
-        this.genotypeStream = genotypeStream;
+        this.genotypeStream = new PrintStream(genotypeStream);
     }
 
     /**

java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java

@@ -31,6 +31,7 @@ import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequence;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
@@ -41,6 +42,7 @@ import java.util.*;
 import java.util.regex.Pattern;
 import java.util.regex.Matcher;
 import java.io.File;
+import java.io.PrintStream;
 
 import net.sf.samtools.util.StringUtil;
 
@@ -50,6 +52,9 @@ import net.sf.samtools.util.StringUtil;
  */
 @Requires({DataSource.READS})
 public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, ClipReadsWalker.ClippingData> {
+    @Output
+    PrintStream out;
+
     /**
      * an optional argument to dump the reads out to a BAM file
      */

java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java

@@ -3,9 +3,11 @@ package org.broadinstitute.sting.gatk.walkers;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.text.DecimalFormat;
 import java.text.NumberFormat;
+import java.io.PrintStream;
 
 
 /*
@@ -41,6 +43,9 @@ import java.text.NumberFormat;
  */
 @Requires({DataSource.READS})
 public class FlagStatWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    PrintStream out;
+
     // what comes out of the flagstat
     static class FlagStat {
         long readCount = 0L;

java/src/org/broadinstitute/sting/gatk/walkers/Multiplex.java

@@ -0,0 +1,43 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers;
+
+import java.lang.annotation.*;
+
+/**
+ * Indicates that the class should be multiplexed according to the rules
+ * specified in the multiplexer.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target({ElementType.FIELD})
+public @interface Multiplex {
+    public Class<? extends Multiplexer> value();
+    public String[] arguments() default {};
+}

java/src/org/broadinstitute/sting/gatk/walkers/Multiplexer.java

@@ -0,0 +1,51 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers;
+
+import java.util.Collection;
+
+/**
+ * An interface for multiplexing output streams.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public interface Multiplexer<T> {
+    /**
+     * Generate a list of the potential outputs that can be created as a function of the other
+     * command-line arguments in this class.
+     * @return A collection of unique identifiers for the file multiplex.
+     */
+    public Collection<T> multiplex();
+
+    /**
+     * Transform the given command-line argument into a suitable form specific to this filename.
+     * @param multiplexedEntry Identifies the individual component of the multiplex.  Will be a value in the collection
+     *        passed back by multiplex().
+     * @param argument The actual command-line argument, supplied for transformation.
+     * @return A transformed representation of the command-line argument.
+     */
+    public String transformArgument(final T multiplexedEntry, final String argument);
+}

java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java

@@ -35,11 +35,13 @@ import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.ArrayList;
 import java.util.List;
+import java.io.PrintStream;
 
 /**
  * Prints the alignment in the pileup format. In the pileup format, each line represents a genomic position,
@@ -60,6 +62,9 @@ import java.util.List;
  * samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
  */
 public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
+    @Output
+    PrintStream out;
+
     @Argument(fullName="alwaysShowSecondBase",doc="If true, prints dummy bases for the second bases in the BAM file where they are missing",required=false)
     public boolean alwaysShowSecondBase = false;
 
@@ -160,4 +165,11 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
 
         return rodString;
     }
+
+    @Override
+    public void onTraversalDone(Integer result) {
+        // Double check traversal result to make count is the same.
+        // TODO: Is this check necessary?
+        out.println("[REDUCE RESULT] Traversal result is: " + result);
+    }    
 }

java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java

@@ -30,14 +30,18 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.Iterator;
+import java.io.PrintStream;
 
 /**
  * Prints out all of the RODs in the input data set. Data is rendered using the toString() method
  * of the given ROD.
  */
 public class PrintRODsWalker extends RodWalker<Integer, Integer> {
+    @Output
+    PrintStream out;
 
     /**
      * Initialize the number of loci processed to zero.

java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java

@@ -33,6 +33,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 
+import java.io.PrintStream;
+
 /**
  * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear
  * in the input file.  It can dynamically merge the contents of multiple input BAM files, resulting
@@ -41,10 +43,9 @@ import org.broadinstitute.sting.commandline.Output;
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
-
     /** an optional argument to dump the reads out to a BAM file */
-    @Output(fullName = "outputBamFile", shortName = "of", doc = "Write output to this BAM filename instead of STDOUT", required = false)
+    @Output(doc="Write output to this BAM filename instead of STDOUT",required=false)
-    SAMFileWriter outputBamFile = null;
+    SAMFileWriter out;
     @Argument(fullName = "readGroup", shortName = "readGroup", doc="Discard reads not belonging to the specified read group", required = false)
     String readGroup = null;
     @Argument(fullName = "platform", shortName = "platform", doc="Discard reads not generated by the specified platform", required = false)
@@ -103,7 +104,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
      * @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
      */
     public SAMFileWriter reduceInit() {
-        return outputBamFile;
+        return out;
     }
 
     /**
@@ -113,12 +114,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
      * @return the SAMFileWriter, so that the next reduce can emit to the same source
      */
     public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
-        if (output != null) {
+        out.addAlignment(read);
-            output.addAlignment(read);
-        } else {
-            out.println(read.format());
-        }
-
         return output;
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java

@@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
@@ -42,6 +43,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 
 import java.util.*;
+import java.io.PrintStream;
 
 /**
  * Converts variants from other file formats to VCF format.
@@ -49,6 +51,8 @@ import java.util.*;
 @Requires(value={},referenceMetaData=@RMD(name=VariantsToVCF.INPUT_ROD_NAME,type= ReferenceOrderedDatum.class))
 @Reference(window=@Window(start=0,stop=40))
 public class VariantsToVCF extends RodWalker<Integer, Integer> {
+    @Output
+    private PrintStream out;
 
     public static final String INPUT_ROD_NAME = "variant";
 
@@ -126,7 +130,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
                 }
             }
 
-            vcfwriter = new VCFWriterImpl(out);
+            vcfwriter = new StandardVCFWriter(out);
             vcfwriter.writeHeader(new VCFHeader(hInfo, samples));
         }
 

java/src/org/broadinstitute/sting/gatk/walkers/Walker.java

@@ -25,16 +25,13 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.io.PrintStream;
 import java.util.List;
-import java.util.ArrayList;
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.filters.MalformedReadFilter;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.apache.log4j.Logger;
-import net.sf.picard.filter.SamRecordFilter;
 
 /**
  * Created by IntelliJ IDEA.
@@ -47,16 +44,6 @@ import net.sf.picard.filter.SamRecordFilter;
 public abstract class Walker<MapType, ReduceType> {
     final protected static Logger logger = Logger.getLogger(Walker.class);
 
-    /**
-     * A stream for writing normal (non-error) output.  System.out by default.
-     */
-    protected PrintStream out = null;
-
-    /**
-     * A stream for writing error output.  System.err by default.
-     */
-    protected PrintStream err = null;
-
     protected Walker() {
     }
 
@@ -134,7 +121,7 @@ public abstract class Walker<MapType, ReduceType> {
     public abstract ReduceType reduce(MapType value, ReduceType sum);    
 
     public void onTraversalDone(ReduceType result) {
-        out.println("[REDUCE RESULT] Traversal result is: " + result);
+        logger.info("[REDUCE RESULT] Traversal result is: " + result);
     }
 
     /**
@@ -143,7 +130,7 @@ public abstract class Walker<MapType, ReduceType> {
      */
     public void onTraversalDone(List<Pair<GenomeLoc, ReduceType>> results) {
         for ( Pair<GenomeLoc, ReduceType> result : results ) {
-            out.printf("[INTERVAL REDUCE RESULT] at %s ", result.getFirst());
+            logger.info(String.format("[INTERVAL REDUCE RESULT] at %s ", result.getFirst()));
             this.onTraversalDone(result.getSecond());
         }
     }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -44,11 +44,13 @@ import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.CommandLineUtils;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 
 import java.util.*;
+import java.io.PrintStream;
 
 
 /**
@@ -59,6 +61,8 @@ import java.util.*;
 @Reference(window=@Window(start=-50,stop=50))
 @By(DataSource.REFERENCE)
 public class VariantAnnotator extends RodWalker<Integer, Integer> {
+    @Output
+    protected PrintStream out;
 
     @Argument(fullName="sampleName", shortName="sample", doc="The sample (NA-ID) corresponding to the variant input (for non-VCF input only)", required=false)
     protected String sampleName = null;
@@ -154,7 +158,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
             hInfo.add(new VCFHeaderLine("VariantAnnotator", "\"" + CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), args, getClass()) + "\""));
         }
 
-        vcfWriter = new VCFWriterImpl(out);
+        vcfWriter = new StandardVCFWriter(out);
         VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
         vcfWriter.writeHeader(vcfHeader);
 

java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java

@@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.EnumMap;
 import java.util.Map;
@@ -47,6 +48,9 @@ import java.io.FileNotFoundException;
  */
 @By(DataSource.REFERENCE)
 public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableBaseState, CallableLociWalker.Integrator> {
+    @Output
+    PrintStream out;
+
     @Argument(fullName = "maxLowMAPQ", shortName = "mlmq", doc = "Maximum value for MAPQ to be considered a problematic mapped read.  The gap between this value and mmq are reads that are not sufficiently well mapped for calling but aren't indicative of mapping problems.", required = false)
     byte maxLowMAPQ = 1;
 

java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java

@@ -31,6 +31,9 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+
+import java.io.PrintStream;
 
 /**
  * Computes the coverage per every <granularity> bases on the reference, or on the subset of the reference
@@ -38,6 +41,8 @@ import org.broadinstitute.sting.commandline.Argument;
  * count anew, even if the count of bases in the last chunk on the previous contig did not reach specified <granularity>.
  */
 public class CoarseCoverageWalker extends ReadWalker<Integer,Integer> {
+    @Output
+    public PrintStream out;
 	
     @Argument(fullName="granularity", shortName="G", doc="Granularity", required=true)
     public Integer N;

java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java

@@ -30,14 +30,19 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broad.tribble.bed.FullBEDFeature;
 
 import java.util.*;
+import java.io.PrintStream;
 
 /**
  * Test routine for new VariantContext object
  */
 public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker.CallableBaseState>, long[][]> {
+    @Output
+    protected PrintStream out;
+
     @Argument(shortName="comp1", doc="First comparison track name", required=false)
     protected String COMP1 = "comp1";
 

java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java

@@ -7,10 +7,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 
-import java.util.HashMap;
+import java.util.*;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
 
 /**
  * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
@@ -41,24 +38,24 @@ public class CoverageUtils {
         return counts;
     }
 
-    public static String getTypeID( SAMReadGroupRecord r, CoverageAggregator.AggregationType type ) {
+    public static String getTypeID( SAMReadGroupRecord r, DoCOutputType.Partition type ) {
-        if ( type == CoverageAggregator.AggregationType.SAMPLE ) {
+        if ( type == DoCOutputType.Partition.sample ) {
             return r.getSample();
-        } else if ( type == CoverageAggregator.AggregationType.READGROUP ) {
+        } else if ( type == DoCOutputType.Partition.readgroup ) {
             return String.format("%s_rg_%s",r.getSample(),r.getReadGroupId());
-        } else if ( type == CoverageAggregator.AggregationType.LIBRARY ) {
+        } else if ( type == DoCOutputType.Partition.library ) {
             return r.getLibrary();
         } else {
             throw new StingException("Invalid type ID sent to getTypeID. This is a BUG!");
         }
     }
 
-    public static Map<CoverageAggregator.AggregationType,Map<String,int[]>>
+    public static Map<DoCOutputType.Partition,Map<String,int[]>>
-                    getBaseCountsByPartition(AlignmentContext context, int minMapQ, int maxMapQ, byte minBaseQ, byte maxBaseQ, List<CoverageAggregator.AggregationType> types) {
+                    getBaseCountsByPartition(AlignmentContext context, int minMapQ, int maxMapQ, byte minBaseQ, byte maxBaseQ, Collection<DoCOutputType.Partition> types) {
 
-        Map<CoverageAggregator.AggregationType,Map<String,int[]>> countsByIDByType = new HashMap<CoverageAggregator.AggregationType,Map<String,int[]>>();
+        Map<DoCOutputType.Partition,Map<String,int[]>> countsByIDByType = new HashMap<DoCOutputType.Partition,Map<String,int[]>>();
         Map<SAMReadGroupRecord,int[]> countsByRG = getBaseCountsByReadGroup(context,minMapQ,maxMapQ,minBaseQ,maxBaseQ);
-        for (CoverageAggregator.AggregationType t : types ) {
+        for (DoCOutputType.Partition t : types ) {
             // iterate through the read group counts and build the type associations
             for ( Map.Entry<SAMReadGroupRecord,int[]> readGroupCountEntry : countsByRG.entrySet() ) {
                 String typeID = getTypeID(readGroupCountEntry.getKey(),t);

java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java

@@ -30,21 +30,18 @@ import org.broad.tribble.FeatureSource;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.TribbleRMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.*;
-import org.broadinstitute.sting.gatk.walkers.By;
+import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.io.File;
 import java.io.IOException;
@@ -67,7 +64,11 @@ import java.util.*;
 // todo -- allow for user to set linear binning (default is logarithmic)
 // todo -- formatting --> do something special for end bins in getQuantile(int[] foo), this gets mushed into the end+-1 bins for now
 @By(DataSource.REFERENCE)
-public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.AggregationType,Map<String,int[]>>, CoverageAggregator> implements TreeReducible<CoverageAggregator> {
+public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partition,Map<String,int[]>>, CoveragePartitioner> implements TreeReducible<CoveragePartitioner> {
+    @Output
+    @Multiplex(value=DoCOutputMultiplexer.class,arguments={"partitionTypes","refSeqGeneList","omitDepthOutput","omitIntervals","omitSampleSummary","omitLocusTable"})
+    Map<DoCOutputType,PrintStream> out;
+    
     @Argument(fullName = "start", doc = "Starting (left endpoint) for granular binning", required = false)
     int start = 1;
     @Argument(fullName = "stop", doc = "Ending (right endpoint) for granular binning", required = false)
@@ -95,7 +96,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
     @Argument(fullName = "omitPerSampleStats", shortName = "omitSampleSummary", doc = "Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.", required = false)
     boolean omitSampleSummary = false;
     @Argument(fullName = "partitionType", shortName = "pt", doc = "Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.", required = false)
-    String[] partitionTypes = new String[] {"sample"};
+    Set<DoCOutputType.Partition> partitionTypes = EnumSet.of(DoCOutputType.Partition.sample);
     @Argument(fullName = "includeDeletions", shortName = "dels", doc = "Include information on deletions", required = false)
     boolean includeDeletions = false;
     @Argument(fullName = "ignoreDeletionSites", doc = "Ignore sites consisting only of deletions", required = false)
@@ -108,10 +109,8 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
     int[] coverageThresholds = {15};
 
     String[] OUTPUT_FORMATS = {"table","rtable","csv"};
-    String[] PARTITION_TYPES = {"sample","readgroup","library"};
     String separator = "\t";
-    List<CoverageAggregator.AggregationType> aggregationTypes = new ArrayList<CoverageAggregator.AggregationType>();
+    Map<DoCOutputType.Partition,List<String>> orderCheck = new HashMap<DoCOutputType.Partition,List<String>>();
-    Map<CoverageAggregator.AggregationType,List<String>> orderCheck = new HashMap<CoverageAggregator.AggregationType,List<String>>();
 
     ////////////////////////////////////////////////////////////////////////////////////
     // STANDARD WALKER METHODS
@@ -145,33 +144,17 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
             separator = ",";
         }
 
-        // Check the partition types
-        for ( String t : partitionTypes ) {
-            boolean valid = false;
-            for ( String s : PARTITION_TYPES ) {
-                if ( s.equalsIgnoreCase(t) ) {
-                    valid = true;
-                }
-            }
-            if ( ! valid ) {
-                throw new StingException("The partition type '"+t+"' is not a valid partition type. Please use any combination of 'sample','readgroup','library'.");
-            } else {
-                aggregationTypes.add(CoverageAggregator.typeStringToAggregationType(t));
-            }
-        }
-
-        if ( getToolkit().getArguments().outFileName == null ) {
-            logger.warn("This walker creates many output files from one input file; you may wish to specify an input file rather "+
-                        "than defaulting all output to stdout.");
-        }
-
         if ( ! omitDepthOutput ) { // print header
+            PrintStream out = getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary);
             out.printf("%s\t%s","Locus","Total_Depth");
-            for (CoverageAggregator.AggregationType type : aggregationTypes ) {
+            for (DoCOutputType.Partition type : partitionTypes ) {
-                out.printf("\t%s_%s","Average_Depth",agTypeToString(type));
+                // mhanna 22 Aug 2010 - Deliberately force this header replacement to make sure integration tests pass.
+                // TODO: Update integration tests and get rid of this.
+                String typeName = (type == DoCOutputType.Partition.readgroup ? "read_group" : type.toString());
+                out.printf("\t%s_%s","Average_Depth",typeName);
             }
             // get all the samples
-            HashSet<String> allSamples = getSamplesFromToolKit(aggregationTypes);
+            HashSet<String> allSamples = getSamplesFromToolKit(partitionTypes);
 
             for ( String s : allSamples) {
                 out.printf("\t%s_%s","Depth_for",s);
@@ -183,10 +166,10 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
             out.printf("%n");
 
         } else {
-            out.printf("Per-Locus Depth of Coverage output was omitted");
+            logger.info("Per-Locus Depth of Coverage output was omitted");
         }
 
-        for (CoverageAggregator.AggregationType type : aggregationTypes ) {
+        for (DoCOutputType.Partition type : partitionTypes ) {
             orderCheck.put(type,new ArrayList<String>());
             for ( String id : getSamplesFromToolKit(type) ) {
                 orderCheck.get(type).add(id);
@@ -195,28 +178,28 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
         }
     }
 
-    private HashSet<String> getSamplesFromToolKit( List<CoverageAggregator.AggregationType> types ) {
+    private HashSet<String> getSamplesFromToolKit( Collection<DoCOutputType.Partition> types ) {
         HashSet<String> partitions = new HashSet<String>(); // since the DOCS object uses a HashMap, this will be in the same order
-        for (CoverageAggregator.AggregationType t : types ) {
+        for (DoCOutputType.Partition t : types ) {
             partitions.addAll(getSamplesFromToolKit(t));
         }
 
         return partitions;
     }
 
-    private HashSet<String> getSamplesFromToolKit(CoverageAggregator.AggregationType type) {
+    private HashSet<String> getSamplesFromToolKit(DoCOutputType.Partition type) {
         HashSet<String> partition = new HashSet<String>();
-        if ( type == CoverageAggregator.AggregationType.SAMPLE ) {
+        if ( type == DoCOutputType.Partition.sample ) {
             for ( Set<String> sampleSet : getToolkit().getSamplesByReaders() ) {
                 for ( String s : sampleSet ) {
                     partition.add(s);
                 }
             }
-        } else if ( type == CoverageAggregator.AggregationType.READGROUP ) {
+        } else if ( type == DoCOutputType.Partition.readgroup ) {
             for ( SAMReadGroupRecord rg : getToolkit().getSAMFileHeader().getReadGroups() ) {
                 partition.add(rg.getSample()+"_rg_"+rg.getReadGroupId());
             }
-        } else if ( type == CoverageAggregator.AggregationType.LIBRARY ) {
+        } else if ( type == DoCOutputType.Partition.library ) {
             for ( Set<String> libraries : getToolkit().getLibrariesByReaders() ) {
                 for ( String l : libraries ) {
                     partition.add(l);
@@ -233,9 +216,9 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
         return ( ! omitIntervals );
     }
 
-    public CoverageAggregator reduceInit() {
+    public CoveragePartitioner reduceInit() {
-        CoverageAggregator aggro = new CoverageAggregator(aggregationTypes,start,stop,nBins);
+        CoveragePartitioner aggro = new CoveragePartitioner(partitionTypes,start,stop,nBins);
-        for (CoverageAggregator.AggregationType t : aggregationTypes ) {
+        for (DoCOutputType.Partition t : partitionTypes ) {
             aggro.addIdentifiers(t,getSamplesFromToolKit(t));
         }
         aggro.initialize(includeDeletions,omitLocusTable);
@@ -243,19 +226,19 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
         return aggro;
     }
 
-    public Map<CoverageAggregator.AggregationType,Map<String,int[]>> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+    public Map<DoCOutputType.Partition,Map<String,int[]>> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
 
         if ( ! omitDepthOutput ) {
-            out.printf("%s",ref.getLocus()); // yes: print locus in map, and the rest of the info in reduce (for eventual cumulatives)
+            getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary).printf("%s",ref.getLocus()); // yes: print locus in map, and the rest of the info in reduce (for eventual cumulatives)
             //System.out.printf("\t[log]\t%s",ref.getLocus());
         }
 
-        return CoverageUtils.getBaseCountsByPartition(context,minMappingQuality,maxMappingQuality,minBaseQuality,maxBaseQuality,aggregationTypes);
+        return CoverageUtils.getBaseCountsByPartition(context,minMappingQuality,maxMappingQuality,minBaseQuality,maxBaseQuality,partitionTypes);
     }
 
-    public CoverageAggregator reduce(Map<CoverageAggregator.AggregationType,Map<String,int[]>> thisMap, CoverageAggregator prevReduce) {
+    public CoveragePartitioner reduce(Map<DoCOutputType.Partition,Map<String,int[]>> thisMap, CoveragePartitioner prevReduce) {
         if ( ! omitDepthOutput ) {
-            printDepths(out,thisMap, prevReduce.getIdentifiersByType());
+            printDepths(getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary),thisMap,prevReduce.getIdentifiersByType());
             // this is an additional iteration through thisMap, plus dealing with IO, so should be much slower without
             // turning on omit
         }
@@ -265,7 +248,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
         return prevReduce;
     }
 
-    public CoverageAggregator treeReduce(CoverageAggregator left, CoverageAggregator right) {
+    public CoveragePartitioner treeReduce(CoveragePartitioner left, CoveragePartitioner right) {
         left.merge(right);
         return left;
     }
@@ -274,55 +257,34 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
     // INTERVAL ON TRAVERSAL DONE
     ////////////////////////////////////////////////////////////////////////////////////
 
-    public void onTraversalDone( List<Pair<GenomeLoc,CoverageAggregator>> statsByInterval ) {
+    public void onTraversalDone( List<Pair<GenomeLoc, CoveragePartitioner>> statsByInterval ) {
-        if ( refSeqGeneList != null && aggregationTypes.contains(CoverageAggregator.AggregationType.SAMPLE ) ) {
+        if ( refSeqGeneList != null && partitionTypes.contains(DoCOutputType.Partition.sample) ) {
             printGeneStats(statsByInterval);
         }
 
-        if ( aggregationTypes.contains(CoverageAggregator.AggregationType.SAMPLE) ) {
+        for(DoCOutputType.Partition partition: partitionTypes) {
-            File intervalStatisticsFile = deriveFromStream("sample_interval_statistics");
+            printIntervalStats(statsByInterval,
-            File intervalSummaryFile = deriveFromStream("sample_interval_summary");
+                    getCorrectStream(partition, DoCOutputType.Aggregation.interval, DoCOutputType.FileType.summary),
-            printIntervalStats(statsByInterval,intervalSummaryFile, intervalStatisticsFile, CoverageAggregator.AggregationType.SAMPLE );
+                    getCorrectStream(partition, DoCOutputType.Aggregation.interval, DoCOutputType.FileType.statistics),
-        }
+                    partition);
-
-        if ( aggregationTypes.contains(CoverageAggregator.AggregationType.READGROUP ) ) {
-            File intervalStatisticsFile = deriveFromStream("read_group_interval_statistics");
-            File intervalSummaryFile = deriveFromStream("read_group_interval_summary");
-            printIntervalStats(statsByInterval,intervalSummaryFile, intervalStatisticsFile, CoverageAggregator.AggregationType.READGROUP);
-        }
-
-        if ( aggregationTypes.contains(CoverageAggregator.AggregationType.LIBRARY) ) {
-            File intervalStatisticsFile = deriveFromStream("library_interval_statistics");
-            File intervalSummaryFile = deriveFromStream("library_interval_summary");
-            printIntervalStats(statsByInterval,intervalSummaryFile,intervalStatisticsFile,CoverageAggregator.AggregationType.LIBRARY);
         }
 
         onTraversalDone(mergeAll(statsByInterval));
 
     }
 
-    public CoverageAggregator mergeAll(List<Pair<GenomeLoc,CoverageAggregator>> stats) {
+    public CoveragePartitioner mergeAll(List<Pair<GenomeLoc, CoveragePartitioner>> stats) {
-        CoverageAggregator first = stats.remove(0).second;
+        CoveragePartitioner first = stats.remove(0).second;
-        for ( Pair<GenomeLoc,CoverageAggregator> iStat : stats ) {
+        for ( Pair<GenomeLoc, CoveragePartitioner> iStat : stats ) {
             treeReduce(first,iStat.second);
         }
 
         return first;
     }
 
-    private DepthOfCoverageStats printIntervalStats(List<Pair<GenomeLoc,CoverageAggregator>> statsByInterval, File summaryFile, File statsFile, CoverageAggregator.AggregationType type) {
+    private DepthOfCoverageStats printIntervalStats(List<Pair<GenomeLoc, CoveragePartitioner>> statsByInterval, PrintStream summaryOut, PrintStream statsOut, DoCOutputType.Partition type) {
-        PrintStream summaryOut;
+        Pair<GenomeLoc, CoveragePartitioner> firstPair = statsByInterval.get(0);
-        PrintStream statsOut;
+        CoveragePartitioner firstAggregator = firstPair.second;
-
-        try {
-            summaryOut = summaryFile == null ? out : new PrintStream(summaryFile);
-            statsOut = statsFile == null ? out : new PrintStream(statsFile);
-        } catch ( IOException e ) {
-            throw new StingException("Unable to open interval file on reduce", e);
-        }
-
-        Pair<GenomeLoc,CoverageAggregator> firstPair = statsByInterval.get(0);
-        CoverageAggregator firstAggregator = firstPair.second;
         DepthOfCoverageStats firstStats = firstAggregator.getCoverageByAggregationType(type);
 
         StringBuilder summaryHeader = new StringBuilder();
@@ -360,7 +322,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
 
         int[][] nTargetsByAvgCvgBySample = new int[firstStats.getHistograms().size()][firstStats.getEndpoints().length+1];
 
-        for ( Pair<GenomeLoc,CoverageAggregator> targetAggregator : statsByInterval ) {
+        for ( Pair<GenomeLoc, CoveragePartitioner> targetAggregator : statsByInterval ) {
 
             Pair<GenomeLoc,DepthOfCoverageStats> targetStats = new Pair<GenomeLoc,DepthOfCoverageStats>(
                     targetAggregator.first, targetAggregator.second.getCoverageByAggregationType(type));
@@ -370,39 +332,29 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
 
         printIntervalTable(statsOut,nTargetsByAvgCvgBySample,firstStats.getEndpoints());
 
-        if ( getToolkit().getArguments().outErrFileName != null && ! getToolkit().getArguments().outFileName.contains("stdout")) {
-            summaryOut.close();
-            statsOut.close();
-        }
-
         return firstStats;
     }
 
-    private void printGeneStats(List<Pair<GenomeLoc,CoverageAggregator>> statsByTarget) {
+    private void printGeneStats(List<Pair<GenomeLoc, CoveragePartitioner>> statsByTarget) {
         LocationAwareSeekableRODIterator refseqIterator = initializeRefSeq();
         List<Pair<String,DepthOfCoverageStats>> statsByGene = new ArrayList<Pair<String,DepthOfCoverageStats>>();// maintains order
         Map<String,DepthOfCoverageStats> geneNamesToStats = new HashMap<String,DepthOfCoverageStats>(); // allows indirect updating of objects in list
 
-        for ( Pair<GenomeLoc,CoverageAggregator> targetStats : statsByTarget ) {
+        for ( Pair<GenomeLoc, CoveragePartitioner> targetStats : statsByTarget ) {
             String gene = getGeneName(targetStats.first,refseqIterator);
             if ( geneNamesToStats.keySet().contains(gene) ) {
-                geneNamesToStats.get(gene).merge(targetStats.second.getCoverageByAggregationType(CoverageAggregator.AggregationType.SAMPLE));
+                geneNamesToStats.get(gene).merge(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample));
             } else {
-                geneNamesToStats.put(gene,new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(CoverageAggregator.AggregationType.SAMPLE)));
+                geneNamesToStats.put(gene,new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample)));
-                statsByGene.add(new Pair<String,DepthOfCoverageStats>(gene,new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(CoverageAggregator.AggregationType.SAMPLE))));
+                statsByGene.add(new Pair<String,DepthOfCoverageStats>(gene,new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample))));
             }
         }
 
-        PrintStream geneSummaryOut = getCorrectStream(out,deriveFromStream("gene_summary"));
+        PrintStream geneSummaryOut = getCorrectStream(DoCOutputType.Partition.sample, DoCOutputType.Aggregation.gene, DoCOutputType.FileType.summary);
 
         for ( Pair<String,DepthOfCoverageStats> geneStats : statsByGene ) {
             printTargetSummary(geneSummaryOut,geneStats);
         }
-
-        if ( ! getToolkit().getArguments().outFileName.contains("stdout")) {
-            geneSummaryOut.close();
-        }
-
     }
 
     //blatantly stolen from Andrew Kernytsky
@@ -530,66 +482,42 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
     // FINAL ON TRAVERSAL DONE
     ////////////////////////////////////////////////////////////////////////////////////
 
-    public void onTraversalDone(CoverageAggregator coverageProfiles) {
+    public void onTraversalDone(CoveragePartitioner coverageProfiles) {
         ///////////////////
         // OPTIONAL OUTPUTS
         //////////////////
 
         if ( ! omitSampleSummary ) {
             logger.info("Printing summary info");
-            for (CoverageAggregator.AggregationType type : aggregationTypes ) {
+            for (DoCOutputType.Partition type : partitionTypes ) {
                 outputSummaryFiles(coverageProfiles,type);
             }
         }
 
         if ( ! omitLocusTable ) {
             logger.info("Printing locus summary");
-            for (CoverageAggregator.AggregationType type : aggregationTypes ) {
+            for (DoCOutputType.Partition type : partitionTypes ) {
                 outputLocusFiles(coverageProfiles,type);
             }
         }
     }
 
-    private String agTypeToString(CoverageAggregator.AggregationType type) {
+    private void outputLocusFiles(CoveragePartitioner coverageProfiles, DoCOutputType.Partition type ) {
-        if ( type == CoverageAggregator.AggregationType.SAMPLE ) {
+        printPerLocus(getCorrectStream(type, DoCOutputType.Aggregation.cumulative, DoCOutputType.FileType.coverage_counts),
-            return "sample";
+                getCorrectStream(type, DoCOutputType.Aggregation.cumulative, DoCOutputType.FileType.coverage_proportions),
-        } else if ( type == CoverageAggregator.AggregationType.READGROUP ) {
+                coverageProfiles.getCoverageByAggregationType(type),type);
-            return "read_group";
-        } else if ( type == CoverageAggregator.AggregationType.LIBRARY ) {
-            return "library";
-        } else {
-            throw new StingException("Invalid aggregation type "+type+" sent to agTypeToString. This is a BUG!");
-        }
     }
 
-    private void outputLocusFiles(CoverageAggregator coverageProfiles, CoverageAggregator.AggregationType type ) {
+    private void outputSummaryFiles(CoveragePartitioner coverageProfiles, DoCOutputType.Partition type ) {
-        File locusStats = deriveFromStream(agTypeToString(type)+"_cumulative_coverage_counts");
+        printPerSample(getCorrectStream(type, DoCOutputType.Aggregation.cumulative, DoCOutputType.FileType.statistics),coverageProfiles.getCoverageByAggregationType(type));
-        File coverageStats = deriveFromStream(agTypeToString(type)+"_cumulative_coverage_proportions");
+        printSummary(getCorrectStream(type, DoCOutputType.Aggregation.cumulative, DoCOutputType.FileType.summary),coverageProfiles.getCoverageByAggregationType(type));
-        printPerLocus(locusStats,coverageStats,coverageProfiles.getCoverageByAggregationType(type),agTypeToString(type));
-    }
-
-    private void outputSummaryFiles(CoverageAggregator coverageProfiles, CoverageAggregator.AggregationType type ) {
-        File summaryFile = deriveFromStream(agTypeToString(type)+"_summary");
-        File statsFile = deriveFromStream(agTypeToString(type)+"_statistics");
-        printPerSample(out,statsFile,coverageProfiles.getCoverageByAggregationType(type));
-        printSummary(out,summaryFile,coverageProfiles.getCoverageByAggregationType(type));
-    }
-
-    public File deriveFromStream(String append) {
-        String name = getToolkit().getArguments().outFileName;
-        if ( name == null || name.contains("stdout") || name.contains("Stdout") || name.contains("STDOUT")) {
-            return null;
-        } else {
-            return new File(name+"."+append);
-        }
     }
 
     ////////////////////////////////////////////////////////////////////////////////////
     // HELPER OUTPUT METHODS
     ////////////////////////////////////////////////////////////////////////////////////
 
-    private void printPerSample(PrintStream out, File optionalFile, DepthOfCoverageStats stats) {
+    private void printPerSample(PrintStream output,DepthOfCoverageStats stats) {
-        PrintStream output = getCorrectStream(out,optionalFile);
         int[] leftEnds = stats.getEndpoints();
 
         StringBuilder hBuilder = new StringBuilder();
@@ -615,13 +543,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
         }
     }
 
-    private void printPerLocus(File locusFile, File coverageFile, DepthOfCoverageStats stats, String partitionType) {
+    private void printPerLocus(PrintStream output, PrintStream coverageOut, DepthOfCoverageStats stats, DoCOutputType.Partition partitionType) {
-        PrintStream output = getCorrectStream(out,locusFile);
-        PrintStream coverageOut = getCorrectStream(out,coverageFile);
-        if ( output == null ) {
-            return;
-        }
-
         int[] endpoints = stats.getEndpoints();
         int samples = stats.getHistograms().size();
 
@@ -634,7 +556,9 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
 
         StringBuilder header = new StringBuilder();
         if ( printSampleColumnHeader ) {
-            header.append(partitionType);
+            // mhanna 22 Aug 2010 - Deliberately force this header replacement to make sure integration tests pass.
+            // TODO: Update integration tests and get rid of this.
+            header.append(partitionType == DoCOutputType.Partition.readgroup ? "read_group" : partitionType.toString());
         }
         header.append(String.format("%sgte_0",separator));
         for ( int d : endpoints ) {
@@ -663,24 +587,14 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
         }
     }
 
-    private PrintStream getCorrectStream(PrintStream out, File optionalFile) {
+    private PrintStream getCorrectStream(DoCOutputType.Partition partition, DoCOutputType.Aggregation aggregation, DoCOutputType.FileType fileType) {
-        PrintStream output;
+        DoCOutputType outputType = new DoCOutputType(partition,aggregation,fileType);
-        if ( optionalFile == null ) {
+        if(!out.containsKey(outputType))
-            output = out;
+            throw new StingException(String.format("Unable to find appropriate stream for partition = %s, aggregation = %s, file type = %s",partition,aggregation,fileType));
-        } else {
+        return out.get(outputType);
-            try {
-                output = new PrintStream(optionalFile);
-            } catch ( IOException e ) {
-                logger.warn("Error opening the output file "+optionalFile.getAbsolutePath()+". Defaulting to stdout");
-                output = out;
-            }
     }
 
-        return output;
+    private void printSummary(PrintStream output, DepthOfCoverageStats stats) {
-    }
-
-    private void printSummary(PrintStream out, File optionalFile, DepthOfCoverageStats stats) {
-        PrintStream output = getCorrectStream(out,optionalFile);
         if ( ! outputFormat.equals("csv") ) {
             output.printf("%s\t%s\t%s\t%s\t%s\t%s","sample_id","total","mean","granular_third_quartile","granular_median","granular_first_quartile");
         } else {
@@ -759,12 +673,12 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
         return 100*( (double) above )/( above + below );
     }
 
-    private void printDepths(PrintStream stream, Map<CoverageAggregator.AggregationType,Map<String,int[]>> countsBySampleByType, Map<CoverageAggregator.AggregationType,List<String>> identifiersByType) {
+    private void printDepths(PrintStream stream, Map<DoCOutputType.Partition,Map<String,int[]>> countsBySampleByType, Map<DoCOutputType.Partition,List<String>> identifiersByType) {
         // get the depths per sample and build up the output string while tabulating total and average coverage
         StringBuilder perSampleOutput = new StringBuilder();
         int tDepth = 0;
         boolean depthCounted = false;
-        for (CoverageAggregator.AggregationType type : aggregationTypes ) {
+        for (DoCOutputType.Partition type : partitionTypes ) {
             Map<String,int[]> countsByID = countsBySampleByType.get(type);
             for ( String s : identifiersByType.get(type) ) {
                 perSampleOutput.append(separator);
@@ -783,7 +697,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
 
         // remember -- genome locus was printed in map()
         stream.printf("%s%d",separator,tDepth);
-        for (CoverageAggregator.AggregationType type : aggregationTypes ) {
+        for (DoCOutputType.Partition type : partitionTypes ) {
             stream.printf("%s%.2f",separator, ( (double) tDepth / identifiersByType.get(type).size() ) );
         }
         stream.printf("%s%n",perSampleOutput);
@@ -818,8 +732,8 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
         return s.toString();
     }
 
-    private void checkOrder(CoverageAggregator ag) {
+    private void checkOrder(CoveragePartitioner ag) {
-        for (CoverageAggregator.AggregationType t : aggregationTypes ) {
+        for (DoCOutputType.Partition t : partitionTypes ) {
             List<String> order = orderCheck.get(t);
             List<String> namesInAg = ag.getIdentifiersByType().get(t);
 
@@ -834,38 +748,105 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
             }
         }
     }
+
 }
 
-class CoverageAggregator {
+class DoCOutputMultiplexer implements Multiplexer<DoCOutputType> {
+    private final Set<DoCOutputType.Partition> partitions;
+    private final File refSeqGeneList;
+    private final boolean omitDepthOutput;
+    private final boolean omitIntervals;
+    private final boolean omitSampleSummary;
+    private final boolean omitLocusTable;
 
-    enum AggregationType { READGROUP, SAMPLE, LIBRARY }
+    /**
+     * Create a new multiplexer type using the values of all variable fields.
+     * @param partitions
+     * @param refSeqGeneList
+     * @param omitDepthOutput
+     * @param omitIntervals
+     * @param omitSampleSummary
+     * @param omitLocusTable
+     */
+    public DoCOutputMultiplexer(final Set<DoCOutputType.Partition> partitions,
+                                final File refSeqGeneList,
+                                final boolean omitDepthOutput,
+                                final boolean omitIntervals,
+                                final boolean omitSampleSummary,
+                                final boolean omitLocusTable) {
+        this.partitions = partitions;
+        this.refSeqGeneList = refSeqGeneList;
+        this.omitDepthOutput = omitDepthOutput;
+        this.omitIntervals = omitIntervals;
+        this.omitSampleSummary = omitSampleSummary;
+        this.omitLocusTable = omitLocusTable;
+    }
 
-    private List<AggregationType> types;
+    public Collection<DoCOutputType> multiplex() {
-    private Map<AggregationType,DepthOfCoverageStats> coverageProfiles;
+        List<DoCOutputType> outputs = new ArrayList<DoCOutputType>();
-    private Map<AggregationType,List<String>> identifiersByType;
+        if(!omitDepthOutput) outputs.add(new DoCOutputType(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary));
+
+        if(!omitIntervals) {
+            for(DoCOutputType.Partition partition: partitions) {
+                outputs.add(new DoCOutputType(partition, DoCOutputType.Aggregation.interval, DoCOutputType.FileType.summary));
+                outputs.add(new DoCOutputType(partition, DoCOutputType.Aggregation.interval, DoCOutputType.FileType.statistics));
+            }
+        }
+
+        if(refSeqGeneList != null && partitions.contains(DoCOutputType.Partition.sample)) {
+            DoCOutputType geneSummaryOut = new DoCOutputType(DoCOutputType.Partition.sample, DoCOutputType.Aggregation.gene, DoCOutputType.FileType.summary);
+            outputs.add(geneSummaryOut);
+        }
+
+        if(!omitSampleSummary) {
+            for(DoCOutputType.Partition partition: partitions) {
+                outputs.add(new DoCOutputType(partition, DoCOutputType.Aggregation.cumulative, DoCOutputType.FileType.summary));
+                outputs.add(new DoCOutputType(partition, DoCOutputType.Aggregation.cumulative, DoCOutputType.FileType.statistics));
+            }
+        }
+
+        if(!omitLocusTable) {
+            for(DoCOutputType.Partition partition: partitions) {
+                outputs.add(new DoCOutputType(partition, DoCOutputType.Aggregation.cumulative, DoCOutputType.FileType.coverage_counts));
+                outputs.add(new DoCOutputType(partition, DoCOutputType.Aggregation.cumulative, DoCOutputType.FileType.coverage_proportions));
+            }
+        }
+
+        return outputs;
+    }
+
+    public String transformArgument(final DoCOutputType outputType, final String argument) {
+        return outputType.getFileName(argument);
+    }
+}
+
+class CoveragePartitioner {
+    private Collection<DoCOutputType.Partition> types;
+    private Map<DoCOutputType.Partition,DepthOfCoverageStats> coverageProfiles;
+    private Map<DoCOutputType.Partition,List<String>> identifiersByType;
     private Set<String> allIdentifiers;
-    public CoverageAggregator(List<AggregationType> typesToUse, int start, int stop, int nBins) {
+    public CoveragePartitioner(Collection<DoCOutputType.Partition> typesToUse, int start, int stop, int nBins) {
-        coverageProfiles = new HashMap<AggregationType,DepthOfCoverageStats>();
+        coverageProfiles = new HashMap<DoCOutputType.Partition,DepthOfCoverageStats>();
-        identifiersByType = new HashMap<AggregationType,List<String>>();
+        identifiersByType = new HashMap<DoCOutputType.Partition,List<String>>();
         types = typesToUse;
-        for ( AggregationType type : types ) {
+        for ( DoCOutputType.Partition type : types ) {
             coverageProfiles.put(type,new DepthOfCoverageStats(DepthOfCoverageStats.calculateBinEndpoints(start,stop,nBins)));
             identifiersByType.put(type,new ArrayList<String>());
         }
         allIdentifiers = new HashSet<String>();
     }
 
-    public void merge(CoverageAggregator otherAggregator) {
+    public void merge(CoveragePartitioner otherAggregator) {
-        for ( AggregationType type : types ) {
+        for ( DoCOutputType.Partition type : types ) {
             this.coverageProfiles.get(type).merge(otherAggregator.coverageProfiles.get(type));
         }
     }
 
-    public DepthOfCoverageStats getCoverageByAggregationType(AggregationType t) {
+    public DepthOfCoverageStats getCoverageByAggregationType(DoCOutputType.Partition t) {
         return coverageProfiles.get(t);
     }
 
-    public void addIdentifiers(AggregationType t, Set<String> ids) {
+    public void addIdentifiers(DoCOutputType.Partition t, Set<String> ids) {
         for ( String s : ids ) {
             coverageProfiles.get(t).addSample(s);
             identifiersByType.get(t).add(s);
@@ -875,7 +856,7 @@ class CoverageAggregator {
     }
 
     public void initialize(boolean useDels, boolean omitLocusTable) {
-        for ( AggregationType t : types ) {
+        for ( DoCOutputType.Partition t : types ) {
             if ( useDels ) {
                 coverageProfiles.get(t).initializeDeletions();
             }
@@ -885,8 +866,8 @@ class CoverageAggregator {
         }
     }
 
-    public void update(Map<AggregationType,Map<String,int[]>> countsByIdentifierByType) {
+    public void update(Map<DoCOutputType.Partition,Map<String,int[]>> countsByIdentifierByType) {
-        for ( AggregationType t : types ) {
+        for ( DoCOutputType.Partition t : types ) {
             coverageProfiles.get(t).update(countsByIdentifierByType.get(t));
         }
     }
@@ -895,23 +876,7 @@ class CoverageAggregator {
         return allIdentifiers;
     }
 
-    public Map<AggregationType,List<String>> getIdentifiersByType() {
+    public Map<DoCOutputType.Partition,List<String>> getIdentifiersByType() {
         return identifiersByType;
     }
-
-    public static AggregationType typeStringToAggregationType(String type) {
-        if ( type.equals("sample") ) {
-            return AggregationType.SAMPLE;
-        }
-
-        if ( type.equals("library") ) {
-            return AggregationType.LIBRARY;
-        }
-
-        if ( type.equals("readgroup") ) {
-            return AggregationType.READGROUP;
-        }
-
-        throw new StingException("Valid partition type string "+type+" is not associated with an aggregation type. This is a BUG!");
-    }
 }

java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java

@@ -0,0 +1,85 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.coverage;
+
+/**
+ * Models a single output file in the DoC walker.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public class DoCOutputType {
+    public enum Partition { readgroup, sample, library }
+    public enum Aggregation { locus, interval, gene, cumulative }
+    public enum FileType { summary, statistics, coverage_counts, coverage_proportions }
+
+    private final Partition partition;
+    private final Aggregation aggregation;
+    private final FileType fileType;
+
+    public DoCOutputType(final Partition partition,
+                         final Aggregation aggregation,
+                         final FileType fileType) {
+        this.partition = partition;
+        this.aggregation = aggregation;
+        this.fileType = fileType;
+    }
+
+    public String getFileName(final String baseName) {
+        // main output
+        if(partition == null)
+            return baseName;
+
+        // mhanna 22 Aug 2010 - Deliberately force this header replacement to make sure integration tests pass.
+        // TODO: Update integration tests and get rid of this.
+        String partitionType = (partition == DoCOutputType.Partition.readgroup ? "read_group" : partition.toString());        
+
+        if(fileType == FileType.coverage_counts || fileType == FileType.coverage_proportions) {
+            // coverage counts / proportions files always include aggregation.
+            return baseName + "." +
+                    partitionType + "_" +
+                    aggregation + "_" +
+                    fileType;
+        }
+
+        return  baseName + "." +
+                partitionType + "_" +
+                (aggregation == Aggregation.interval || aggregation == Aggregation.gene ? aggregation + "_" : "") +
+                fileType;
+    }
+
+    public int hashCode() {
+        return (partition!=null?partition.ordinal()+1:0) * aggregation.ordinal() * fileType.ordinal();
+    }
+
+    public boolean equals(Object other) {
+        if(!(other instanceof DoCOutputType))
+            return false;
+        DoCOutputType otherOutputType = (DoCOutputType)other;
+        return partition == otherOutputType.partition &&
+                aggregation == otherOutputType.aggregation &&
+                fileType == otherOutputType.fileType;
+    }
+}

java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java

@@ -32,6 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import net.sf.samtools.SAMRecord;
 
 import java.io.*;
@@ -42,6 +43,8 @@ import java.io.*;
  */
 @WalkerName("BamToFastq")
 public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    private PrintStream out;
 
     @Argument(fullName="re_reverse", shortName="reverse", doc="re-reverse bases and quals of reads from the negative strand", required=false)
     private Boolean RE_REVERSE = false;

java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java

@@ -34,6 +34,9 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+
+import java.io.PrintStream;
 
 /**
  * Renders a new reference in FASTA format consisting of only those loci provided in the input data set.  Has optional
@@ -41,6 +44,7 @@ import org.broadinstitute.sting.commandline.Argument;
  */
 @WalkerName("FastaReferenceMaker")
 public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
+    @Output PrintStream out;
     @Argument(fullName="lineWidth", shortName="lw", doc="Maximum length of sequence to write per line", required=false) public int fastaLineWidth=60;
     @Argument(fullName="rawOnelineSeq", shortName="raw", doc="Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity) - CAUTION: adjacent intervals will automatically be merged", required=false) public boolean fastaRawSeqs=false;
 

java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -38,11 +38,13 @@ import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.CommandLineUtils;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 
 import java.util.*;
+import java.io.PrintStream;
 
 
 /**
@@ -51,6 +53,8 @@ import java.util.*;
 @Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
 @Reference(window=@Window(start=-50,stop=50))
 public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
+    @Output
+    protected PrintStream out;
 
     @Argument(fullName="filterExpression", shortName="filter", doc="One or more expression used with INFO fields to filter (see wiki docs for more info)", required=false)
     protected ArrayList<String> FILTER_EXPS = new ArrayList<String>();
@@ -119,7 +123,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
             hInfo.add(new VCFHeaderLine("VariantFiltration", "\"" + CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), args, getClass()) + "\""));
         }
 
-        writer = new VCFWriterImpl(out);
+        writer = new StandardVCFWriter(out);
         writer.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(vc.getSampleNames())));
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/CreateTriggerTrack.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.Collection;
 import java.io.PrintWriter;
@@ -37,13 +38,9 @@ import java.io.PrintWriter;
  * Creates a bed-format trigger-track for the Unified Genotyper based on input variant files.
  */
 public class CreateTriggerTrack extends RodWalker<Integer, Integer> {
-
+    @Output
     private PrintWriter writer;
 
-    public void initialize() {
-        writer = new PrintWriter(out);
-    }
-
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if ( tracker == null )
             return 0;

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -38,6 +38,8 @@ import org.broadinstitute.sting.utils.genotype.vcf.*;
 
 import java.util.*;
 import java.io.PrintStream;
+import java.io.File;
+import java.io.FileNotFoundException;
 
 
 /**
@@ -54,10 +56,10 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     public VCFWriter writer = null;
 
     @Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false)
-    protected PrintStream verboseWriter = null;
+    protected File verboseFile = null;
 
     @Argument(fullName = "metrics_file", shortName = "metrics", doc = "File to print any relevant callability metrics output", required = false)
-    protected PrintStream metricsWriter = null;
+    protected File metricsFile = null;
 
     @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
     protected List<String> annotationsToUse = new ArrayList<String>();
@@ -81,6 +83,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     // enable extended events for indels
     public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS; }
 
+    private PrintStream verboseWriter;
+    private PrintStream metricsWriter;
+
     /**
      * Inner class for collecting output statistics from the UG
      */
@@ -110,6 +115,18 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
      *
      **/
     public void initialize() {
+        try {
+            if(verboseWriter != null) verboseWriter = new PrintStream(verboseFile);
+        }
+        catch(FileNotFoundException ex) {
+            throw new StingException("Unable to create verbose writer from provided file "+verboseFile,ex);
+        }
+        try {
+            if(metricsWriter != null) metricsWriter = new PrintStream(metricsFile);
+        }
+        catch(FileNotFoundException ex) {
+            throw new StingException("Unable to create metrics writer from provided file "+metricsFile,ex);
+        }
 
         annotationEngine = new VariantAnnotatorEngine(getToolkit(), Arrays.asList(annotationClassesToUse), annotationsToUse);
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, verboseWriter, annotationEngine);

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java

@@ -52,6 +52,7 @@ import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.collections.CircularArray;
 import org.broadinstitute.sting.utils.collections.PrimitivePair;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.io.File;
 import java.io.IOException;
@@ -70,6 +71,9 @@ import java.util.*;
  */
 @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, PlatformUnitFilter.class})
 public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
+    @Output
+    PrintStream out;
+
     @Argument(fullName="outputFile", shortName="O", doc="output file name (defaults to BED format)", required=true)
     java.io.File bed_file;
 

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -46,6 +46,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.io.File;
 import java.io.FileWriter;
+import java.io.PrintStream;
 import java.util.*;
 
 /**
@@ -69,6 +70,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     @Argument(fullName="entropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false)
     protected double MISMATCH_THRESHOLD = 0.15;
 
+    @Output
+    protected PrintStream out;
+
+    @Output(fullName = "err", shortName = "e", doc = "An error output file presented to the walker.  Will overwrite contents if file exists.", required = false)
+    protected PrintStream err;
+
     @Output(fullName="output", shortName="O", required=false, doc="Output bam")
     protected String writerFilename = null;
 

java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java

@@ -37,12 +37,14 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.ArrayList;
+import java.io.PrintStream;
 
 /**
  * Emits intervals for the Local Indel Realigner to target for cleaning.  Ignores 454 and MQ0 reads.
@@ -52,6 +54,8 @@ import java.util.ArrayList;
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @By(DataSource.REFERENCE)
 public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Event, RealignerTargetCreator.Event> {
+    @Output
+    protected PrintStream out;
 
     // mismatch/entropy/SNP arguments
     @Argument(fullName="windowSize", shortName="window", doc="window size for calculating entropy or SNP clusters", required=false)

java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java

@@ -29,7 +29,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
@@ -50,8 +49,6 @@ public class CountRodByRefWalker extends RefWalker<CountRodWalker.Datum, Pair<Ex
     public void initialize() {
         crw.verbose = verbose;
         crw.showSkipped = showSkipped;
-        JVMUtils.setFieldValue(JVMUtils.findField(CountRodWalker.class,"out"),crw,out);
-        JVMUtils.setFieldValue(JVMUtils.findField(CountRodWalker.class,"err"),crw,err);
     }
 
     public CountRodWalker.Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {

java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java

@@ -35,17 +35,22 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Collection;
 import java.util.LinkedList;
+import java.io.PrintStream;
 
 /**
  * Prints out counts of the number of reference ordered data objects are
  * each locus for debugging RodWalkers.
  */
 public class CountRodWalker extends RodWalker<CountRodWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
+    @Output
+    public PrintStream out;
+
     @Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false)
     public boolean verbose = false;
 

java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java

@@ -34,14 +34,12 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.PrimitivePair;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
 
 import java.util.*;
-import java.io.File;
+import java.io.*;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.BufferedWriter;
 
 /**
  * Created by IntelliJ IDEA.
@@ -58,6 +56,9 @@ import java.io.BufferedWriter;
  */
 @Requires({DataSource.READS})
 public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
+    @Output
+    protected PrintStream out;
+
     @Argument(fullName="mappedOnly", shortName="mo", doc="when this flag is set (default), statistics will be collected "+
                 "on mapped reads only, while unmapped reads will be discarded", required=false)
     protected boolean MAPPED_ONLY = true;

java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java

@@ -4,9 +4,11 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.List;
 import java.util.Arrays;
+import java.io.PrintStream;
 
 import net.sf.samtools.SAMRecord;
 
@@ -15,6 +17,9 @@ import net.sf.samtools.SAMRecord;
  * all aligning reads in a compact but human-readable form. 
  */
 public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integer> implements TreeReducible<Integer> {
+    @Output
+    private PrintStream out;
+
     public AlignmentContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         out.printf( "In map: ref = %s, loc = %s, reads = %s%n", ref.getBaseAsChar(),
                                                                 context.getLocation(),

java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java

@@ -32,13 +32,11 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import net.sf.samtools.*;
 
 import java.util.*;
-import java.io.File;
+import java.io.*;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.BufferedWriter;
 
 /**
  * User: depristo
@@ -52,6 +50,9 @@ import java.io.BufferedWriter;
  */
 @Requires({DataSource.READS})
 public class ReadClippingStatsWalker extends ReadWalker<ReadClippingStatsWalker.ReadClippingInfo,Integer> {
+    @Output
+    protected PrintStream out;
+
     @Argument(fullName="mappedOnly", shortName="mo", doc="when this flag is set (default), statistics will be collected "+
                 "on mapped reads only, while unmapped reads will be discarded", required=false)
     protected boolean MAPPED_ONLY = true;

java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java

@@ -35,9 +35,11 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.Arrays;
+import java.io.PrintStream;
 
 /**
  * At every locus in the input set, compares the pileup data (reference base, aligned base from
@@ -46,6 +48,9 @@ import java.util.Arrays;
  */
 @Requires(value={DataSource.READS,DataSource.REFERENCE},referenceMetaData=@RMD(name="pileup",type=SAMPileupFeature.class))
 public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats>  implements TreeReducible<ValidationStats> {
+    @Output
+    private PrintStream out;
+
     @Argument(fullName="continue_after_error",doc="Continue after an error",required=false)
     public boolean CONTINUE_AFTER_AN_ERROR = false;
 

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java

@@ -83,6 +83,9 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
     /////////////////////////////
     @ArgumentCollection private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
 
+    @Output
+    PrintStream out;
+
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.PrintStream;
 import java.util.*;
 import java.util.regex.Pattern;
 
@@ -81,6 +82,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     @Input(fullName="recal_file", shortName="recalFile", required=false, doc="Filename for the input covariates table recalibration .csv file")
     public File RECAL_FILE = new File("output.recal_data.csv");
 
+    @Output
+    private PrintStream out;
+
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////

java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java

@@ -5,11 +5,16 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.commandline.Output;
+
+import java.io.PrintStream;
 
 /**
  * Create a mask for use with the PickSequenomProbes walker.
  */
 public class CreateSequenomMask extends RodWalker<Integer, Integer> {
+    @Output
+    PrintStream out;
 
     public void initialize() {}
 

java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java

@@ -43,10 +43,12 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.Collection;
+import java.io.PrintStream;
 
 
 /**
@@ -57,6 +59,9 @@ import java.util.Collection;
 @Requires(value={DataSource.REFERENCE})
 @Reference(window=@Window(start=-200,stop=200))
 public class PickSequenomProbes extends RodWalker<String, String> {
+    @Output
+    PrintStream out;
+
     @Argument(required=false, shortName="snp_mask", doc="positions to be masked with N's")
     protected String SNP_MASK = null;
     @Argument(required=false, shortName="project_id",doc="If specified, all probenames will be prepended with 'project_id|'")

java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java

@@ -39,10 +39,12 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 
 import java.util.*;
+import java.io.PrintStream;
 
 /**
  * Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes)
@@ -50,6 +52,9 @@ import java.util.*;
 @Reference(window=@Window(start=0,stop=40))
 @Requires(value={},referenceMetaData=@RMD(name="sequenom",type= ReferenceOrderedDatum.class))
 public class SequenomValidationConverter extends RodWalker<Pair<VariantContext, Byte>,Integer> {
+    @Output
+    protected PrintStream out;
+
     @Argument(fullName="maxHardy", doc="Maximum phred-scaled Hardy-Weinberg violation pvalue to consider an assay valid [default:20]", required=false)
     protected double maxHardy = 20.0;
     @Argument(fullName="maxNoCall", doc="Maximum no-call rate (as a fraction) to consider an assay valid [default:0.05]", required=false)
@@ -119,7 +124,7 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
         if ( sampleNames == null )
             sampleNames = new TreeSet<String>();
 
-        VCFWriter vcfWriter = new VCFWriterImpl(out);
+        VCFWriter vcfWriter = new StandardVCFWriter(out);
 
         // set up the info and filter headers
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -47,8 +47,9 @@ import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
 import java.io.File;
@@ -110,6 +111,9 @@ import java.util.*;
  */
 @Reference(window=@Window(start=-50,stop=50))
 public class VariantEvalWalker extends RodWalker<Integer, Integer> {
+    @Output
+    protected PrintStream out;
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // walker arguments
@@ -341,7 +345,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
         determineContextNamePartSizes();
 
         if ( outputVCF != null )
-            writer = new VCFWriterImpl(new File(outputVCF));
+            writer = new StandardVCFWriter(new File(outputVCF));
 
         if ( rsIDFile != null ) {
             if ( maxRsIDBuild == Integer.MAX_VALUE )

java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java

@@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
 import java.io.File;
@@ -157,7 +157,7 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFInfoHeaderLine("OQ", 1, VCFHeaderLineType.Float, "The original variant quality score"));
         hInfo.add(new VCFHeaderLine("source", "VariantOptimizer"));
-        vcfWriter = new VCFWriterImpl( new File(OUTPUT_FILENAME) );
+        vcfWriter = new StandardVCFWriter( new File(OUTPUT_FILENAME) );
         final TreeSet<String> samples = new TreeSet<String>();
         samples.addAll(SampleUtils.getSampleListWithVCFHeader(getToolkit(), null));
         

java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java

@@ -41,7 +41,7 @@ import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 
 import java.io.File;
 import java.io.IOException;
@@ -138,7 +138,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         hInfo.add(new VCFHeaderLine("source", "VariantOptimizer"));
         samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit()));
 
-        vcfWriter = new VCFWriterImpl( new File(OUTPUT_PREFIX + ".vcf") );
+        vcfWriter = new StandardVCFWriter( new File(OUTPUT_PREFIX + ".vcf") );
         final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
         vcfWriter.writeHeader(vcfHeader);
 

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java

@@ -39,10 +39,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
 import java.util.*;
+import java.io.PrintStream;
 
 /**
  * Combines VCF records from different sources; supports both full merges and set unions.
@@ -53,6 +55,9 @@ import java.util.*;
 @Reference(window=@Window(start=-50,stop=50))
 @Requires(value={})
 public class CombineVariants extends RodWalker<Integer, Integer> {
+    @Output
+    private PrintStream out;
+
     // the types of combinations we currently allow
     @Argument(shortName="genotypeMergeOptions", doc="How should we merge genotype records for samples shared across the ROD files?", required=false)
     public VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE;
@@ -81,7 +86,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
     private VariantAnnotatorEngine engine;
 
     public void initialize() {
-        vcfWriter = new VCFWriterImpl(out);
+        vcfWriter = new StandardVCFWriter(out);
         validateAnnotateUnionArguments();
 
         Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null);

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java

@@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -34,15 +34,19 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.commandline.Output;
 import org.broad.tribble.vcf.VCFHeader;
 
 import java.util.*;
+import java.io.PrintStream;
 
 /**
  * Filters a lifted-over VCF file for ref bases that have been changed.
  */
 @Requires(value={},referenceMetaData=@RMD(name="variant",type= ReferenceOrderedDatum.class))
 public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
+    @Output
+    PrintStream out;
 
     private VCFWriter writer;
 
@@ -52,7 +56,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
         Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));
 
-        writer = new VCFWriterImpl(out);
+        writer = new StandardVCFWriter(out);
         final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey("variant") ? vcfHeaders.get("variant").getMetaData() : null, samples);
         writer.writeHeader(vcfHeader);
     }

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java

@@ -26,9 +26,10 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -40,6 +41,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils
 import org.broad.tribble.vcf.VCFHeader;
 
 import java.io.File;
+import java.io.PrintStream;
 import java.util.*;
 
 import net.sf.picard.liftover.LiftOver;
@@ -52,6 +54,8 @@ import net.sf.samtools.SAMFileReader;
  */
 @Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
 public class LiftoverVariants extends RodWalker<Integer, Integer> {
+    @Output
+    protected PrintStream out;
 
     @Argument(fullName="chain", shortName="chain", doc="Chain file", required=true)
     protected File CHAIN = null;
@@ -75,7 +79,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
         Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));
 
-        writer = new VCFWriterImpl(out);
+        writer = new StandardVCFWriter(out);
         final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey("variant") ? vcfHeaders.get("variant").getMetaData() : null, samples);
         writer.writeHeader(vcfHeader);
     }

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -28,9 +28,8 @@ import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFHeaderLine;
-import org.broad.tribble.vcf.VCFHeaderLineType;
-import org.broad.tribble.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
@@ -40,15 +39,15 @@ import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import java.io.PrintStream;
 import java.io.File;
 import java.io.FileNotFoundException;
 
@@ -58,6 +57,9 @@ import java.io.FileNotFoundException;
  */
 @Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
 public class SelectVariants extends RodWalker<Integer, Integer> {
+    @Output
+    private PrintStream out;
+
     @Argument(fullName="sample", shortName="sn", doc="Sample(s) to include.  Can be a single sample, specified multiple times for many samples, a file containing sample names, a regular expression to select many samples, or any combination thereof.", required=false)
     public Set<String> SAMPLE_EXPRESSIONS;
 
@@ -83,7 +85,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
      * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
      */
     public void initialize() {
-        vcfWriter = new VCFWriterImpl(out);
+        vcfWriter = new StandardVCFWriter(out);
 
         ArrayList<String> rodNames = new ArrayList<String>();
         rodNames.add("variant");

java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlignedReadsHistoWalker.java

@@ -5,6 +5,9 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.commandline.Output;
+
+import java.io.PrintStream;
 
 /**
  * Created by IntelliJ IDEA.
@@ -15,6 +18,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
  */
 @WalkerName("Aligned_Reads_Histogram")
 public class AlignedReadsHistoWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    PrintStream out;
+
     long[] alignCounts = new long[51];
 
     public void initialize() {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/AlleleBalanceHistogramWalker.java

@@ -12,8 +12,10 @@ import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.*;
+import java.io.PrintStream;
 
 /**
  * Created by IntelliJ IDEA.
@@ -24,7 +26,8 @@ import java.util.*;
  */
 @Requires(value= DataSource.REFERENCE,referenceMetaData = {@RMD(name="variants",type=ReferenceOrderedDatum.class)})
 public class AlleleBalanceHistogramWalker extends LocusWalker<Map<String,Double>, Map<String,Set<Double>>> {
-
+    @Output
+    PrintStream out;
 
     public Map<String,Set<Double>> reduceInit() {
         return new HashMap<String,Set<Double>>();

java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java

@@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -50,6 +51,9 @@ import net.sf.samtools.SAMRecord;
 @By(DataSource.REFERENCE)
 @Reference(window=@Window(start=-3,stop=3))
 public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<BaseTransitionTable>,Set<BaseTransitionTable>> implements TreeReducible<Set<BaseTransitionTable>> {
+    @Output
+    PrintStream out;
+
     @Argument(fullName="usePreviousBases", doc="Use previous bases of the reference as part of the calculation, uses the specified number, defaults to 0", required=false)
     int nPreviousBases = 0;
     @Argument(fullName="useSecondaryBase",doc="Use the secondary base of a read as part of the calculation", required=false)

java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java

@@ -30,6 +30,7 @@ import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFConstants;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -55,6 +56,9 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
 
     private boolean newLine = true;
 
+    @Output
+    public PrintStream out;
+
     @Argument(fullName = "output_file", shortName = "output", doc = "File to output results", required = true)
     public PrintStream outputWriter = null;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/CountIntervals.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -12,6 +13,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.util.List;
+import java.io.PrintStream;
 
 /**
  * Counts the number of contiguous regions the walker traverses over. Slower than it needs to be, but
@@ -19,6 +21,9 @@ import java.util.List;
  * This was its very first use.
  */
 public class CountIntervals extends RefWalker<Long, Long> {
+    @Output
+    PrintStream out;
+
     @Argument(fullName="numOverlaps",shortName="no",doc="Count all occurrences of X or more overlapping intervals; defaults to 2", required=false)
     int numOverlaps = 2;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/CreateTiTvTrack.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
@@ -11,6 +12,7 @@ import org.broadinstitute.sting.utils.wiggle.WiggleHeader;
 import org.broadinstitute.sting.utils.wiggle.WiggleWriter;
 
 import java.util.ArrayList;
+import java.io.PrintStream;
 
 /**
  * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
@@ -19,6 +21,9 @@ import java.util.ArrayList;
  * @Date Jul 21, 2010
  */
 public class CreateTiTvTrack extends RodWalker<VariantContext,TiTvWindow> {
+    @Output
+    PrintStream out;
+
     @Argument(shortName="size",doc="Size of the window",required = true)
     int size = -1;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DSBWalkerV3.java

@@ -29,11 +29,13 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import net.sf.samtools.SAMRecord;
 
 import java.util.*;
+import java.io.PrintStream;
 
 /**
  * Created by IntelliJ IDEA.
@@ -43,6 +45,8 @@ import java.util.*;
  * To change this template use File | Settings | File Templates.
  */
 public class DSBWalkerV3 extends ReadWalker<Integer,Integer> {
+    @Output
+    PrintStream out;
 
     @Argument(fullName="windowSize",shortName="W",doc="Size of the sliding window",required=true)
     int WINDOW_SIZE = 100;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DbSNPWindowCounter.java

@@ -7,6 +7,7 @@ import org.broad.tribble.dbsnp.DbSNPCodec;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broad.tribble.iterators.CloseableTribbleIterator;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -20,6 +21,7 @@ import org.broadinstitute.sting.utils.StingException;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.PrintStream;
 
 /**
  * DbSNPWindowCounter
@@ -37,6 +39,9 @@ public class DbSNPWindowCounter extends LocusWalker<Integer, Long> {
     // what we read in new tracks with
     private FeatureSource reader;
     
+    @Output
+    private PrintStream out;
+
     @Argument(fullName = "dbSNPFile", shortName = "db", doc="The dbsnp file to search upstream and downstream for nearby snps", required = true)
     private File myDbSNPFile;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java

@@ -10,8 +10,10 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.*;
+import java.io.PrintStream;
 
 /**
  * Takes an interval list and annotates intervals with genes and exons falling within that interval
@@ -28,6 +30,9 @@ public class DesignFileGeneratorWalker extends RodWalker<Long,Long> {
     private HashSet<RefSeqFeature> refseqBuffer = new HashSet<RefSeqFeature>();
     private HashMap<String,BEDFeature> currentBedFeatures = new HashMap<String,BEDFeature>();
 
+    @Output
+    PrintStream out;
+
     public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         // three items to look up: interval_list, refseq, gene*
         if ( tracker == null ) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ErrorRatePerReadPosition.java

@@ -6,10 +6,12 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.List;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.io.PrintStream;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
@@ -18,6 +20,7 @@ import net.sf.samtools.SAMReadGroupRecord;
  * Computes the read error rate per position in read (in the original 5'->3' orientation that the read had coming off the machine)
  */
 public class ErrorRatePerReadPosition extends LocusWalker<Integer, Integer> {
+    @Output PrintStream out;
     @Argument(fullName="min_base_quality_score", shortName="mbq", doc="Minimum base quality required to consider a base for calling (default: 0)", required=false) public Integer MIN_BASE_QUAL = 0;
     @Argument(fullName="min_mapping_quality_score", shortName="mmq", doc="Minimum read mapping quality required to consider a read for calling (default: 0)", required=false) public Integer MIN_MAPPING_QUAL = 0;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/GCCalculatorWalker.java

@@ -10,11 +10,13 @@ import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
+import java.io.PrintStream;
 
 /**
  * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
@@ -23,6 +25,8 @@ import java.util.Set;
  * @Date May 19, 2010
  */
 public class GCCalculatorWalker extends RefWalker<Pair<Set<GenomeLoc>,Boolean>, Map<GenomeLoc,Pair<Long,Long>>> {
+    @Output
+    PrintStream out;
 
     public Map<GenomeLoc,Pair<Long,Long>> reduceInit() {
         return new HashMap<GenomeLoc,Pair<Long,Long>>();

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java

@@ -4,6 +4,7 @@ import org.broad.tribble.FeatureSource;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
@@ -21,6 +22,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.*;
 
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintStream;
 import java.util.*;
 
 /**
@@ -30,6 +32,8 @@ import java.util.*;
  * @Date Apr 21, 2010
  */
 public class IndelAnnotator extends RodWalker<Integer,Long>{
+    @Output
+    PrintStream out;
     @Argument(fullName="refseq", shortName="refseq",
 			doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated with GENOMIC/UTR/INTRON/CODING and with the gene name", required=true)
 	String RefseqFileName = null;
@@ -85,7 +89,7 @@ public class IndelAnnotator extends RodWalker<Integer,Long>{
         anno.add(new VCFInfoHeaderLine("type",1, VCFHeaderLineType.String,"Genomic interpretation (according to RefSeq)"));
         hInfo.addAll(anno);
 
-        vcfWriter = new VCFWriterImpl(out);
+        vcfWriter = new StandardVCFWriter(out);
         VCFHeader vcfHeader = new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit()));
         vcfWriter.writeHeader(vcfHeader);
     }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java

@@ -4,6 +4,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
@@ -17,7 +18,7 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 
 import java.io.PrintStream;
 import java.util.*;
@@ -30,7 +31,8 @@ import java.util.*;
  */
 @Reference(window=@Window(start=-40,stop=40))
 public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator> {
-
+    @Output
+    PrintStream out;
     @Argument(fullName="indelWindow",doc="size of the window in which to look for indels; max 40",required=false)
     int indelWindow = 10;
     @Argument(fullName="writeVCF",doc="Writes \"overlapping\" variants to this vcf",required=false)
@@ -47,7 +49,7 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
         }
 
         if ( outVCF != null ) {
-            vcfWriter = new VCFWriterImpl(outVCF);
+            vcfWriter = new StandardVCFWriter(outVCF);
             Set<VCFHeaderLine> header = new HashSet<VCFHeaderLine>();
             header.addAll(VCFUtils.getHeaderFields(getToolkit()));
             VCFHeader vcfHeader = new VCFHeader(header, SampleUtils.getUniqueSamplesFromRods(getToolkit()));

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelErrorRateWalker.java

@@ -38,10 +38,12 @@ import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.List;
 import java.util.LinkedList;
 import java.util.Iterator;
+import java.io.PrintStream;
 
 /**
  * Created by IntelliJ IDEA.
@@ -52,6 +54,8 @@ import java.util.Iterator;
  */
 @Reference(window=@Window(start=-10,stop=10))
 public class IndelErrorRateWalker extends LocusWalker<Integer,Integer> {
+    @Output
+    PrintStream out;
     @Argument(fullName="minCoverage",shortName="minC",doc="Assess only sites with coverage at or above the specified value.",required=true)
     int MIN_COVERAGE = 0;
     @Argument(fullName="maxCoverage",shortName="maxC",doc="Assess only sites with coverage at or below the specified value.",required=false)

java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java

@@ -6,6 +6,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
@@ -23,7 +24,7 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 
 import java.io.PrintStream;
@@ -39,6 +40,8 @@ import java.util.*;
  * @Date Jun 8, 2010
  */
 public class MendelianViolationClassifier extends LocusWalker<MendelianViolationClassifier.MendelianViolation, VCFWriter> {
+    @Output
+    PrintStream out;
     @Argument(shortName="f",fullName="familyPattern",required=true,doc="Pattern for the family structure (usage: mom+dad=child)")
     String familyStr = null;
     @Argument(shortName="ob",fullName="outputBed",required=true,doc="Output file to write the homozygous region information to")
@@ -373,7 +376,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
      *********** REDUCE INIT
      */
     public VCFWriter reduceInit() {
-        VCFWriter writer = new VCFWriterImpl(out);
+        VCFWriter writer = new StandardVCFWriter(out);
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFHeaderLine("source", "MendelianViolationClassifier"));

java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchCounterWalker.java

@@ -6,11 +6,16 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.List;
+import java.io.PrintStream;
 
 @WalkerName("CountMismatches")
 public class MismatchCounterWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    PrintStream out;
+
     public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         int nMismatches = 0;
         

java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchHistoWalker.java

@@ -6,12 +6,16 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.List;
 import static java.lang.reflect.Array.*;
+import java.io.PrintStream;
 
 @WalkerName("Mismatch_Histogram")
 public class MismatchHistoWalker extends ReadWalker<Integer, Integer> { 
+    @Output
+    PrintStream out;
 
     protected long[] mismatchCounts = new long[0];
     protected final int MIN_TARGET_EDIT_DISTANCE = 5;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/NeighborhoodQualityWalker.java

@@ -4,10 +4,12 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.commandline.Output;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 import java.util.Iterator;
+import java.io.PrintStream;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -71,6 +73,8 @@ import java.util.Iterator;
  */
 
 public class NeighborhoodQualityWalker extends LocusWalker<Integer, Long> {
+    @Output
+    PrintStream out;
 
     public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
         float neighborhoodQualityScore = 0.0f;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/PairedQualityScoreCountsWalker.java

@@ -33,8 +33,11 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import net.sf.samtools.SAMRecord;
 
+import java.io.PrintStream;
+
 /**
  * This walker prints out quality score counts for first and second reads of a pair aggregated over all reads
  * in the interval.
@@ -42,6 +45,9 @@ import net.sf.samtools.SAMRecord;
  * @Author: Chris Hartl
  */
 public class PairedQualityScoreCountsWalker extends ReadWalker<Pair<byte[],Boolean>,Pair<CycleQualCounts,CycleQualCounts>> {
+    @Output
+    public PrintStream out;
+
     @Argument(fullName="readLength", shortName="rl", doc="Length of reads in the bam file", required=true)
     public int readLength = -1;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
@@ -37,6 +38,7 @@ import net.sf.samtools.SAMRecord;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Random;
+import java.io.PrintStream;
 
 /**
  * ReadErrorRateWalker assesses the error rate per read position ('cycle') by comparing the
@@ -48,6 +50,7 @@ import java.util.Random;
  * @author Kiran Garimella
  */
 public class ReadErrorRateWalker extends ReadWalker<boolean[], ReadErrorRateCollection> implements TreeReducible<ReadErrorRateCollection> {
+    @Output PrintStream out;
     @Argument(fullName="printVisualHits",   shortName="v",  doc="print visual hits",    required=false) public boolean printVisualHits = false;
     @Argument(fullName="useNextBestBase",   shortName="nb", doc="use next best base",   required=false) public boolean useNextBestBase = false;
     @Argument(fullName="useNonNextBestBase",shortName="nnb",doc="use nonnext best base",required=false) public boolean useNonNextBestBase = false;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadQualityScoreWalker.java

@@ -29,16 +29,14 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileWriter;
 
-import java.io.FileReader;
+import java.io.*;
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.IOException;
 
 /**
  * Created by IntelliJ IDEA.
@@ -61,6 +59,8 @@ import java.io.IOException;
  */
 
 public class ReadQualityScoreWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
+    @Output
+    protected PrintStream out;
     @Argument(fullName = "inputQualityFile", shortName = "if", doc = "Input quality score file generated by NeighborhoodQualityWalker", required = true)
     protected String inputQualityFile = null;
     @Argument(fullName = "outputBamFile", shortName = "of", doc = "Write output to this BAM filename instead of STDOUT", required = false)

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.java

@@ -29,11 +29,13 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.collections.Pair;
 import net.sf.samtools.*;
 
 import java.util.HashMap;
 import java.io.File;
+import java.io.PrintStream;
 
 /**
  * ReadErrorRateWalker assesses the error rate per read position ('cycle') by comparing the
@@ -45,6 +47,9 @@ import java.io.File;
  * @author Kiran Garimella
  */
 public class ReplaceQuals extends ReadWalker<SAMRecord, SAMFileWriter> {
+    @Output
+    public PrintStream out;
+
     @Argument(shortName="inputQualsBAM",doc="BAM files containing qualities to be replaced",required=true)
     public String inputQualsBAM;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java

@@ -33,6 +33,7 @@ import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -44,6 +45,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.PrintStream;
 import java.util.Scanner;
 import java.util.TreeMap;
 import java.util.SortedMap;
@@ -60,6 +62,9 @@ public class TestReadFishingWalker extends ReadWalker<Integer,Long> {
      */
     private BWAAligner aligner;
 
+    @Output
+    private PrintStream out;
+
     @Argument(fullName="indel_calls",shortName="ic",doc="Indel calls to use to derive custom references",required=true)
     private File indelCalls;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java

@@ -32,14 +32,19 @@ import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.EnumSet;
 import java.io.File;
+import java.io.PrintStream;
 
 /**
  * Test routine for new VariantContext object
  */
 public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
+    @Output
+    PrintStream out;
+
     @Argument(fullName="takeFirstOnly", doc="Only take the first second at a locus, as opposed to all", required=false)
     boolean takeFirstOnly = false;
 
@@ -60,7 +65,7 @@ public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
 
     public void initialize() {
         if ( outputVCF != null )
-            writer = new VCFWriterImpl(new File(outputVCF));
+            writer = new StandardVCFWriter(new File(outputVCF));
     }
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@@ -100,4 +105,11 @@ public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
     public Integer reduce(Integer point, Integer sum) {
         return point + sum;
     }
+
+    @Override
+    public void onTraversalDone(Integer result) {
+        // Double check traversal result to make count is the same.
+        // TODO: Is this check necessary?
+        out.println("[REDUCE RESULT] Traversal result is: " + result);
+    }
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java

@@ -4,6 +4,7 @@ import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
@@ -14,11 +15,12 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
+import java.io.PrintStream;
 import java.util.*;
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -53,6 +55,9 @@ import java.util.*;
 public class VCF4WriterTestWalker extends RodWalker<Integer, Integer> {
     private VCFWriter vcfWriter;
 
+    @Output
+    private PrintStream out;
+
     @Argument(fullName="output_file", shortName="output", doc="VCF file to which output should be written", required=true)
     private String OUTPUT_FILE = null;
 
@@ -80,7 +85,7 @@ public class VCF4WriterTestWalker extends RodWalker<Integer, Integer> {
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
 
 
-        vcfWriter = new VCFWriterImpl(new File(OUTPUT_FILE));
+        vcfWriter = new StandardVCFWriter(new File(OUTPUT_FILE));
         VCFHeader header = null;
         for( final ReferenceOrderedDataSource source : dataSources ) {
             final RMDTrack rod = source.getReferenceOrderedData();

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ValidateRODForReads.java

@@ -7,11 +7,13 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.Map;
+import java.io.PrintStream;
 
 /**
  * validate the rods for reads
@@ -20,6 +22,9 @@ public class ValidateRODForReads extends ReadWalker<Integer, Integer> {
     // a mapping of the position to the count of rods
     HashMap<GenomeLoc, Integer> map = new LinkedHashMap<GenomeLoc, Integer>();
 
+    @Output
+    private PrintStream out;
+
     @Override
     public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
         if (tracker != null) {

java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java

@@ -29,6 +29,7 @@ import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
@@ -44,7 +45,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
+import org.broadinstitute.sting.utils.genotype.vcf.StandardVCFWriter;
 import org.broad.tribble.vcf.*;
 
 import java.io.*;
@@ -65,6 +66,9 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
     public static final String PROBS_ROD_NAME = "beagleProbs";
     public static final String PHASED_ROD_NAME = "beaglePhased";
 
+    @Output
+    private PrintStream out;
+
     @Argument(fullName="output_file", shortName="output", doc="VCF file to which output should be written", required=true)
     private String OUTPUT_FILE = null;
 
@@ -93,7 +97,7 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
         hInfo.add(new VCFHeaderLine("source", "BeagleImputation"));
 
         // Open output file specified by output VCF ROD
-        vcfWriter = new VCFWriterImpl(new File(OUTPUT_FILE));
+        vcfWriter = new StandardVCFWriter(new File(OUTPUT_FILE));
         final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
 
         for( final ReferenceOrderedDataSource source : dataSources ) {

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java

@@ -30,12 +30,14 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Enumeration;
 import java.util.Vector;
 import java.util.Collections;
+import java.io.PrintStream;
 
 /**
  * Calculates likelihood of observing the data given pairs of HLA alleles. NOTE: run CalculateBaseLikelihoods first! Usage: java -jar GenomeAnalysisTK.jar -T CalculateAlleleLikelihoods -I /humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.nuc.imputed.4digit.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -bl INPUT.baselikelihoods -eth\
@@ -44,6 +46,9 @@ nicity Caucasian | grep -v "INFO"  | grep -v "DONE!" > OUTPUT.allelelikelihoods
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CalculateAlleleLikelihoodsWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    public PrintStream out;
+
     @Argument(fullName = "baseLikelihoods", shortName = "bl", doc = "Base likelihoods file", required = true)
     public String baseLikelihoodsFile = "";
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java

@@ -35,15 +35,21 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.io.PrintStream;
+
 /**
  * Calculates the probability of observing data for each genotype at every position. NOTE: run FindClosestAllele first to create .filter file. Usage: java -jar GenomeAnalysisTK.jar -T CalculateBaseLikelihoods -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval [-filter INPUT.filter -minAllowedMismatches 7] | grep -v "INFO" | grep -v "MISALIGNED" > OUTPUT.baselikelihoods
  * @author shermanjia
  */
 public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Long, Long>>{
+    @Output
+    public PrintStream out;
+
     @Argument(fullName = "debugHLA", shortName = "debugHLA", doc = "Print debug", required = false)
     public boolean DEBUG = false;
     @Argument(fullName = "debugAlleles", shortName = "debugAlleles", doc = "Print likelihood scores for these alleles", required = false)

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java

@@ -37,11 +37,9 @@ import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
-import java.io.BufferedReader;
+import java.io.*;
-import java.io.DataInputStream;
-import java.io.FileInputStream;
-import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
@@ -51,6 +49,9 @@ import java.util.List;
  * @author shermanjia
  */
 public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
+    @Output
+    public PrintStream out;
+
     @Argument(fullName="suppressLocusPrinting",doc="Suppress printing",required=false)
     public boolean suppressPrinting = false;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/ClusterReadsWalker.java

@@ -5,15 +5,21 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.io.PrintStream;
+
 /**
  * Compares reads to longest read at each exon. Usage: java -jar GenomeAnalysisTK.jar -T ClusterReads -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta [-filter INPUT.filter] | grep -v INFO | sort -k1 > OUTPUT
  * @author shermanjia
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class ClusterReadsWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    public PrintStream out;
+
     @Argument(fullName = "filter", shortName = "filter", doc = "file containing reads to exclude", required = false)
     public String filterFile = "";
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreateHaplotypesWalker.java

@@ -4,14 +4,20 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.Hashtable;
+import java.io.PrintStream;
+
 /**
  * Creates a haplotype file given reads (for SNP analysis, imputation, etc)
  * @author shermanjia
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CreateHaplotypesWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    PrintStream out;
+
     CigarParser formatter = new CigarParser();
     char c;
     boolean DEBUG = false;

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java

@@ -30,10 +30,13 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Enumeration;
+import java.io.PrintStream;
+
 /**
  * Creates a ped file of SNPs and amino acids coded as SNPs given an input ped file with 4-digit HLA alleles. Usage: java -jar GenomeAnalysisTK.jar -T CreatePedFile --allelesFile INPUT.ped -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-sc\
 r1/GSA/sjia/454_HLA/HLA/HLA.combined.4digitUnique.bam > OUTPUT.log
@@ -41,6 +44,9 @@ r1/GSA/sjia/454_HLA/HLA/HLA.combined.4digitUnique.bam > OUTPUT.log
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    public PrintStream out;
+
     @Argument(fullName = "allelesFile", shortName = "allelesFile", doc = "Create ped file for HLA alleles named in this file", required = true)
     public String alleleNamesFile = "";
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestHLAWalker.java

@@ -30,15 +30,21 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.io.PrintStream;
+
 /**
  * Finds the most similar HLA allele for each read (helps detect misalignments). Usage: java -jar GenomeAnalysisTK.jar -T FindClosestHLA -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L INPUT.interval | grep -v INFO | sort -k1 > OUTPUT
  * @author shermanjia
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class FindClosestHLAWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    protected PrintStream out;
+
     @Argument(fullName = "debugRead", shortName = "debugRead", doc = "Print match score for read", required = false)
     public String debugRead = "";
 
@@ -300,5 +306,12 @@ public class FindClosestHLAWalker extends ReadWalker<Integer, Integer> {
     public Integer reduce(Integer value, Integer sum) {
         return value + sum;
     }
+
+    @Override
+    public void onTraversalDone(Integer result) {
+        // Double check traversal result to make count is the same.
+        // TODO: Is this check necessary?
+        out.println("[REDUCE RESULT] Traversal result is: " + result);
+    }    
 }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindPolymorphicSitesWalker.java

@@ -5,15 +5,21 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.io.PrintStream;
+
 /**
  * Finds polymorphic sites in the HLA dictionary. Usage: java -jar GenomeAnalysisTK.jar -T FindPolymorphicSites -I HLA_DICTIONARY.bam -R /broad/1KG/reference/human_b36_both.fasta -L INPUT.interval -findFirst | grep -v INFO | sort -k1 > OUTPUT
  * @author shermanjia
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class FindPolymorphicSitesWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    public PrintStream out;
+
     @Argument(fullName = "debugRead", shortName = "debugRead", doc = "Print match score for read", required = false)
     public String debugRead = "";
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerWalker.java

@@ -31,9 +31,11 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 
 import java.util.*;
 import java.util.Map.Entry;
+import java.io.PrintStream;
 
 /**
  * Calculates the likelihood of observing data given phase info from pairs of HLA alleles. Note: Run FindClosestAlleleWalker first! Usage: java -jar $GATK -T HLACaller -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -phaseInterval /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -bl IMPUT.baselikelihoods [-filter $ID.filter -minAllowe\
@@ -42,6 +44,9 @@ dMismatches 7] -ethnicity Caucasian | grep -v "INFO"  | grep -v "DEBUG" | grep -
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class HLACallerWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    private PrintStream out;
+
     @Argument(fullName = "baseLikelihoods", shortName = "bl", doc = "Base likelihoods file", required = true)
     public String baseLikelihoodsFile = "";
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/ImputeAllelesWalker.java

@@ -4,11 +4,9 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.commandline.Output;
 
-import java.io.FileInputStream;
+import java.io.*;
-import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.Hashtable;
 /**
@@ -17,6 +15,9 @@ import java.util.Hashtable;
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class ImputeAllelesWalker extends ReadWalker<Integer, Integer> {
+    @Output
+    PrintStream out;           
+
     String HLAdatabaseFile ="/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA_DICTIONARY.sam";
 //    String ClosestAllelesFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.CLASS1.closest";
     String ClosestAllelesFile = "/humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.CLASS2.closest";