The engine now automatically adds the command-line arguments to the header of every VCF, unless -NO_HEADER is specified.

Changed integration tests, adding the -NO_HEADER argument, for walkers that previously did not include the command-line
arg headers.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4326 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -48,7 +48,7 @@ public class CommandLineUtils {
      * @return A key-value mapping of argument full names to argument values.  Produces best string representation
      *         possible given the information available.
      */
-    public static Map<String,String> getApproximateCommandLineArguments(Collection<Object> argumentProviders) {
+    public static Map<String,String> getApproximateCommandLineArguments(Object... argumentProviders) {
         Map<String,String> commandLineArguments = new LinkedHashMap<String,String>();
 
         for(Object argumentProvider: argumentProviders) {
@@ -67,47 +67,23 @@ public class CommandLineUtils {
         return commandLineArguments;
     }
 
-//    public static Map<String,String> getApproximateCommandLineArguments(Collection<Object> argumentProviders) {
+    /**
-//        Map<String,String> commandLineArguments = new LinkedHashMap<String,String>();
+     * Create an approximate list of command-line arguments based on the given argument providers.
-//
+     * @param argumentProviders Argument providers to inspect.
-//        for(Object argumentProvider: argumentProviders) {
+     * @return A string representing the given command-line arguments.
-//            Map<ArgumentSource, Object> argBings = ParsingEngine.extractArgumentBindings(argumentProvider);
+     */
-//            List<ArgumentSource> argumentSources = ParsingEngine.extractArgumentSources(argumentProvider.getClass());
+    public static String createApproximateCommandLineArgumentString(Object... argumentProviders) {
-//            for(ArgumentSource argumentSource: argumentSources) {
+        Map<String,String> commandLineArgs = getApproximateCommandLineArguments(argumentProviders);
-//                Object argumentValue = JVMUtils.getFieldValue(argumentSource.field,argumentProvider);
-//                String argumentValueString = argumentValue != null ? argumentValue.toString() : null;
-//
-//                for(ArgumentDefinition definition: argumentSource.createArgumentDefinitions()) {
-//                    String argumentName = definition.fullName;
-//                    commandLineArguments.put(argumentName,argumentValueString);
-//                }
-//            }
-//        }
-//
-//        return commandLineArguments;
-//    }
-
-    public static String createApproximateCommandLineArgumentString(GenomeAnalysisEngine toolkit, Walker walker) {
-        return createApproximateCommandLineArgumentString(toolkit, null, walker);
-    }
-
-    public static String createApproximateCommandLineArgumentString(GenomeAnalysisEngine toolkit, Collection<Object> otherArgumentProviders, Walker walker) {
         StringBuffer sb = new StringBuffer();
-        sb.append("analysis_type=");
-        sb.append(toolkit.getWalkerName(walker.getClass()));
-
-        ArrayList<Object> allArgumentProviders = new ArrayList<Object>();
-        allArgumentProviders.add(toolkit.getArguments());
-        allArgumentProviders.add(walker);
-        if (otherArgumentProviders != null) allArgumentProviders.addAll(otherArgumentProviders);
-
-        Map<String,String> commandLineArgs = getApproximateCommandLineArguments(allArgumentProviders);
 
+        boolean first = true;
         for ( Map.Entry<String, String> commandLineArg : commandLineArgs.entrySet() ) {
-            sb.append(" ");
+            if(!first)
+                sb.append(" ");
             sb.append(commandLineArg.getKey());
             sb.append("=");
             sb.append(commandLineArg.getValue());
+            first = false;
         }
 
         return sb.toString();

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

@@ -368,23 +368,6 @@ public class ParsingEngine {
         return new ArrayList<ArgumentSource>(bindings.keySet());
     }
 
-//        List<ArgumentSource> argumentSources = new ArrayList<ArgumentSource>();
-//        while( sourceClass != null ) {
-//            Field[] fields = sourceClass.getDeclaredFields();
-//            for( Field field: fields ) {
-//                if( ArgumentTypeDescriptor.isArgumentAnnotationPresent(field) )
-//                    argumentSources.add( new ArgumentSource(parentFields, field) );
-//                if( field.isAnnotationPresent(ArgumentCollection.class) ) {
-//                    Field[] newParentFields = Arrays.copyOf(parentFields, parentFields.length + 1);
-//                    newParentFields[parentFields.length] = field;
-//                    argumentSources.addAll( extractArgumentSources(field.getType(), newParentFields) );
-//                }
-//            }
-//            sourceClass = sourceClass.getSuperclass();
-//        }
-//        return argumentSources;
-//    }
-
     public static Map<ArgumentSource, Object> extractArgumentBindings(Object obj) {
         if ( obj == null ) throw new IllegalArgumentException("Incoming object cannot be null");
         return extractArgumentBindings(obj, obj.getClass(), new Field[0]);

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

@@ -28,6 +28,10 @@ package org.broadinstitute.sting.gatk;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
+import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
+import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
+import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
+import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 
@@ -39,15 +43,13 @@ import net.sf.picard.filter.SamRecordFilter;
  * @author aaron
  */
 public abstract class CommandLineExecutable extends CommandLineProgram {
-    public Object GATKResult = null;
-
     /**
      * The actual engine which performs the analysis.
      */
-    protected GenomeAnalysisEngine GATKEngine = new GenomeAnalysisEngine();
+    protected GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
 
     // get the analysis name
-    protected abstract String getAnalysisName();
+    public abstract String getAnalysisName();
 
     /**
      * Gets the GATK argument bundle.
@@ -55,8 +57,10 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      */
     protected abstract GATKArgumentCollection getArgumentCollection();
 
-    // override select arguments
+    /**
-    protected void overrideArguments() { }
+     * A list of all the arguments initially used as sources.
+     */
+    private final Collection<Object> argumentSources = new ArrayList<Object>();
 
     /**
      * this is the function that the inheriting class can expect to have called
@@ -65,21 +69,30 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      * @return the return code to exit the program with
      */
     protected int execute() throws Exception {
-        Walker<?,?> mWalker = GATKEngine.getWalkerByName(getAnalysisName());
+        argumentSources.add(this);
+
+        Walker<?,?> walker = engine.getWalkerByName(getAnalysisName());
 
         try {
-            Collection<SamRecordFilter> filters = GATKEngine.createFiltersForWalker(getArgumentCollection(),mWalker);
+            Collection<SamRecordFilter> filters = engine.createFiltersForWalker(getArgumentCollection(),walker);
 
             // load the arguments into the walker / filters.
-            loadArgumentsIntoObject(mWalker);
+            // TODO: The fact that this extra load call exists here when all the parsing happens at the engine
-            for (SamRecordFilter filter: filters)
+            // TODO: level indicates that we're doing something wrong.  Turn this around so that the GATK can drive
+            // TODO: argument processing.
+            loadArgumentsIntoObject(walker);
+            argumentSources.add(walker);
+
+            for (SamRecordFilter filter: filters) {
                 loadArgumentsIntoObject(filter);
+                argumentSources.add(filter);
+            }
 
             // set the analysis name in the argument collection
-            GATKResult = GATKEngine.execute(getArgumentCollection(), mWalker, filters);
+            engine.execute(getArgumentCollection(), walker, filters);
-            generateGATKRunReport(mWalker);
+            generateGATKRunReport(walker);
         } catch ( Exception e ) {
-            generateGATKRunReport(mWalker, e);
+            generateGATKRunReport(walker, e);
             throw e;
         }
 
@@ -94,9 +107,9 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      *
      * @param e the exception, can be null if no exception occurred
      */
-    private void generateGATKRunReport(Walker<?,?> mWalker, Exception e) {
+    private void generateGATKRunReport(Walker<?,?> walker, Exception e) {
         if ( getArgumentCollection().phoneHomeType != GATKRunReport.PhoneHomeOption.NO_ET ) {
-            GATKRunReport report = new GATKRunReport(mWalker, e, GATKEngine, getArgumentCollection().phoneHomeType );
+            GATKRunReport report = new GATKRunReport(walker, e, engine, getArgumentCollection().phoneHomeType );
             if ( getArgumentCollection().phoneHomeType == GATKRunReport.PhoneHomeOption.STDOUT )
                 report.postReport(System.out);
             else
@@ -108,10 +121,10 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      * Convenience method for fully parameterized generateGATKRunReport when an exception has
      * not occurred
      * 
-     * @param mWalker
+     * @param walker
      */
-    private void generateGATKRunReport(Walker<?,?> mWalker) {
+    private void generateGATKRunReport(Walker<?,?> walker) {
-        generateGATKRunReport(mWalker, null);
+        generateGATKRunReport(walker, null);
     }
 
     /**
@@ -119,7 +132,10 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      * @return A collection of type descriptors generating implementation-dependent placeholders.
      */
     protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() {
-        return GATKEngine.getArgumentTypeDescriptors();
+        return Arrays.asList( new VCFWriterArgumentTypeDescriptor(engine,System.out,argumentSources),
+                              new SAMFileReaderArgumentTypeDescriptor(engine),
+                              new SAMFileWriterArgumentTypeDescriptor(engine,System.out),
+                              new OutputStreamArgumentTypeDescriptor(engine,System.out) );
     }
 
     /**
@@ -143,10 +159,10 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
 
         Collection<Class> argumentSources = new ArrayList<Class>();
 
-        Walker walker = GATKEngine.getWalkerByName(getAnalysisName());
+        Walker walker = engine.getWalkerByName(getAnalysisName());
         argumentSources.add(walker.getClass());
 
-        Collection<SamRecordFilter> filters = GATKEngine.createFiltersForWalker(getArgumentCollection(),walker);
+        Collection<SamRecordFilter> filters = engine.createFiltersForWalker(getArgumentCollection(),walker);
         for(SamRecordFilter filter: filters)
             argumentSources.add(filter.getClass());
 
@@ -156,7 +172,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
 
     @Override
     protected String getArgumentSourceName( Class argumentSource ) {
-        return GATKEngine.getWalkerName((Class<Walker>)argumentSource);
+        return engine.getWalkerName((Class<Walker>)argumentSource);
     }
 
     /**
@@ -166,6 +182,6 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      */
     @Override
     protected void addTags(Object key, List<String> tags) {
-        GATKEngine.addTags(key,tags);
+        engine.addTags(key,tags);
     }
-}
+        }

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

@@ -66,7 +66,7 @@ public class CommandLineGATK extends CommandLineExecutable {
     }
 
     @Override
-    protected String getAnalysisName() {
+    public String getAnalysisName() {
         return analysisName;
     }
 
@@ -132,7 +132,7 @@ public class CommandLineGATK extends CommandLineExecutable {
         String additionalHelp;
 
         // If no analysis name is present, fill in extra help on the walkers.
-        WalkerManager walkerManager = GATKEngine.getWalkerManager();
+        WalkerManager walkerManager = engine.getWalkerManager();
         String analysisName = getAnalysisName();
         if(analysisName != null && walkerManager.exists(getAnalysisName()))
             additionalHelp = getWalkerHelp(walkerManager.getWalkerClassByName(getAnalysisName()));
@@ -153,7 +153,7 @@ public class CommandLineGATK extends CommandLineExecutable {
 
         formatter.format("Description:%n");
 
-        WalkerManager walkerManager = GATKEngine.getWalkerManager();
+        WalkerManager walkerManager = engine.getWalkerManager();
         String walkerHelpText = walkerManager.getWalkerDescriptionText(walkerType);
 
         printDescriptorLine(formatter,WALKER_INDENT,"",WALKER_INDENT,FIELD_SEPARATOR,walkerHelpText,TextFormattingUtils.DEFAULT_LINE_WIDTH);
@@ -173,7 +173,7 @@ public class CommandLineGATK extends CommandLineExecutable {
         formatter.format("Available analyses:%n");
 
         // Get the list of walker names from the walker manager.
-        WalkerManager walkerManager = GATKEngine.getWalkerManager();
+        WalkerManager walkerManager = engine.getWalkerManager();
 
         // Build a list sorted by walker display name.  As this information is collected, keep track of the longest
         // package / walker name for later formatting.

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

@@ -563,19 +563,6 @@ 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.
      *

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

@@ -144,7 +144,6 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
      * @return Argument definition for the BAM file itself.  Will not be null.
      */
     private ArgumentDefinition createBAMCompressionArgumentDefinition(ArgumentSource source) {
-        Annotation annotation = getArgumentAnnotation(source);
         return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
                                        int.class,
                                        COMPRESSION_FULLNAME,
@@ -161,7 +160,6 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     }
 
     private ArgumentDefinition createWriteIndexArgumentDefinition(ArgumentSource source) {
-        Annotation annotation = getArgumentAnnotation(source);
         return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
                                        boolean.class,
                                        CREATE_INDEX_FULLNAME,

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

@@ -25,15 +25,18 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
+import org.broad.tribble.vcf.VCFHeaderLine;
 import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.OutputStream;
-import java.util.List;
+import java.lang.annotation.Annotation;
-import java.util.Arrays;
+import java.util.*;
-import java.util.HashSet;
 
 /**
  * Injects new command-line arguments into the system providing support for the genotype writer.
@@ -42,8 +45,9 @@ import java.util.HashSet;
  * @version 0.1
  */
 public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
-
+    private static final String NO_HEADER_ARG_NAME = "NO_HEADER";
     private static final HashSet<String> SUPPORTED_ZIPPED_SUFFIXES = new HashSet<String>();
+
     //
     // static list of zipped suffixes supported by this system.
     //
@@ -55,21 +59,28 @@ public class VCFWriterArgumentTypeDescriptor 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;
 
+    /**
+     * The sources into which arguments were injected.
+     */
+    private final Collection<Object> argumentSources;
+
     /**
      * 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.
+     * @param argumentSources sources from which command-line arguments should be derived.
      */
-    public VCFWriterArgumentTypeDescriptor(GenomeAnalysisEngine engine, OutputStream defaultOutputStream) {
+    public VCFWriterArgumentTypeDescriptor(GenomeAnalysisEngine engine, OutputStream defaultOutputStream, Collection<Object> argumentSources) {
         this.engine = engine;
         this.defaultOutputStream = defaultOutputStream;
+        this.argumentSources = argumentSources;
     }
 
     /**
@@ -84,7 +95,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
 
     @Override
     public List<ArgumentDefinition> createArgumentDefinitions( ArgumentSource source ) {
-        return Arrays.asList( createDefaultArgumentDefinition(source) );
+        return Arrays.asList( createDefaultArgumentDefinition(source),createNoHeaderArgumentDefinition());
     }
 
     /**
@@ -98,7 +109,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
 
     @Override
     public Object createTypeDefault(ArgumentSource source,Class type) {
-        VCFWriterStub stub = new VCFWriterStub(defaultOutputStream, false);
+        VCFWriterStub stub = new VCFWriterStub(defaultOutputStream, false, argumentSources, false);
         engine.addOutput(stub);
         return stub;
     }
@@ -119,8 +130,11 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         // Should we compress the output stream?
         boolean compress = writerFileName != null && SUPPORTED_ZIPPED_SUFFIXES.contains(getFileSuffix(writerFileName));
 
+        boolean skipWritingHeader = argumentIsPresent(createNoHeaderArgumentDefinition(),matches);
+
         // Create a stub for the given object.
-        VCFWriterStub stub = (writerFile != null) ? new VCFWriterStub(writerFile, compress) : new VCFWriterStub(System.out, compress);
+        VCFWriterStub stub = (writerFile != null) ? new VCFWriterStub(writerFile, compress, argumentSources, skipWritingHeader)
+                                                  : new VCFWriterStub(defaultOutputStream, compress, argumentSources, skipWritingHeader);
 
         // WARNING: Side effects required by engine!
         parsingEngine.addTags(stub,getArgumentTags(matches));
@@ -129,6 +143,27 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
         return stub;
     }
 
+    /**
+     * Creates the optional compression level argument for the BAM file.
+     * @return Argument definition for the BAM file itself.  Will not be null.
+     */
+    private ArgumentDefinition createNoHeaderArgumentDefinition() {
+        return new ArgumentDefinition( ArgumentIOType.ARGUMENT,
+                                       boolean.class,
+                                       NO_HEADER_ARG_NAME,
+                                       NO_HEADER_ARG_NAME,
+                                       "Don't output the usual VCF header tag with the command line. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.",
+                                       false,
+                                       true,
+                                       false,
+                                       true,
+                                       null,
+                                       null,
+                                       null,
+                                       null );
+    }
+
+
     /**
      * Returns a lower-cased version of the suffix of the provided file.
      * @param fileName the file name.  Must not be null.
@@ -140,4 +175,5 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             return "";
         return fileName.substring(indexOfLastDot).toLowerCase();
     }
+
 }

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

@@ -28,11 +28,18 @@ package org.broadinstitute.sting.gatk.io.stubs;
 import java.io.File;
 import java.io.PrintStream;
 import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.TreeSet;
 
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFHeader;
+import org.broad.tribble.vcf.VCFHeaderLine;
 import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.commandline.CommandLineUtils;
+import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
 
 /**
  * A stub for routing and management of genotype reading and writing.
@@ -55,7 +62,7 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
     private final PrintStream genotypeStream;
 
     /**
-     * The cached VCF header (initilized to null)
+     * The cached VCF header (initialized to null)
      */
     private VCFHeader vcfHeader = null;
 
@@ -64,6 +71,17 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
      */
     private final boolean isCompressed;
 
+    /**
+     * A hack: push the argument sources into the VCF header so that the VCF header
+     * can rebuild the command-line arguments.
+     */
+    private final Collection<Object> argumentSources;
+
+    /**
+     * Should the header be written out?  A hidden argument.
+     */
+    private final boolean skipWritingHeader;
+
     /**
      * Connects this stub with an external stream capable of serving the
      * requests of the consumer of this stub.
@@ -75,10 +93,12 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
      * @param genotypeFile  file to (ultimately) create.
      * @param isCompressed  should we compress the output stream?
      */
-    public VCFWriterStub(File genotypeFile, boolean isCompressed) {
+    public VCFWriterStub(File genotypeFile, boolean isCompressed, Collection<Object> argumentSources, boolean skipWritingHeader) {
         this.genotypeFile = genotypeFile;
         this.genotypeStream = null;
         this.isCompressed = isCompressed;
+        this.argumentSources = argumentSources;
+        this.skipWritingHeader = skipWritingHeader;
     }
 
     /**
@@ -86,10 +106,12 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
      * @param genotypeStream  stream to (ultimately) write.
      * @param isCompressed  should we compress the output stream?
      */
-    public VCFWriterStub(OutputStream genotypeStream, boolean isCompressed) {
+    public VCFWriterStub(OutputStream genotypeStream, boolean isCompressed, Collection<Object> argumentSources, boolean skipWritingHeader) {
         this.genotypeFile = null;
         this.genotypeStream = new PrintStream(genotypeStream);
         this.isCompressed = isCompressed;
+        this.argumentSources = argumentSources;
+        this.skipWritingHeader = skipWritingHeader;
     }
 
     /**
@@ -134,7 +156,18 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
 
     public void writeHeader(VCFHeader header) {
         vcfHeader = header;
-        outputTracker.getStorage(this).writeHeader(header);
+
+        // Check for the command-line argument header line.  If not present, add it in.
+        VCFHeaderLine commandLineArgHeaderLine = getCommandLineArgumentHeaderLine();
+        boolean foundCommandLineHeaderLine = false;
+        for(VCFHeaderLine line: vcfHeader.getMetaData()) {
+            if(line.getKey().equals(commandLineArgHeaderLine.getKey()))
+                foundCommandLineHeaderLine = true;
+        }
+        if(!foundCommandLineHeaderLine && !skipWritingHeader)
+            vcfHeader.addMetaDataLine(commandLineArgHeaderLine);
+
+        outputTracker.getStorage(this).writeHeader(vcfHeader);
     }
 
     /**
@@ -150,4 +183,22 @@ public class VCFWriterStub implements Stub<VCFWriter>, VCFWriter {
     public void close() {
         outputTracker.getStorage(this).close();
     }
+
+    /**
+     * Gets a string representation of this object.
+     * @return
+     */
+    @Override
+    public String toString() {
+        return getClass().getName();
+    }
+
+    /**
+     * Gets the appropriately formatted header for a VCF file
+     * @return VCF file header.
+     */
+    private VCFHeaderLine getCommandLineArgumentHeaderLine() {
+        CommandLineExecutable executable = JVMUtils.getObjectOfType(argumentSources,CommandLineExecutable.class);
+        return new VCFHeaderLine(executable.getAnalysisName(), "\"" + CommandLineUtils.createApproximateCommandLineArgumentString(argumentSources) + "\"");
+    }
 }

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

@@ -80,9 +80,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
     @Argument(fullName="vcfContainsOnlyIndels", shortName="dels",doc="Use if you are annotating an indel vcf, currently VERY experimental", required = false)
     protected boolean indelsOnly = false;
 
-    @Argument(fullName = "NO_HEADER", shortName = "NO_HEADER", doc = "Don't output the usual VCF header tag with the command line. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.", required = false)
-    protected Boolean NO_VCF_HEADER_LINE = false;
-
     private HashMap<String, String> nonVCFsampleName = new HashMap<String, String>();
 
     private VariantAnnotatorEngine engine;
@@ -145,9 +142,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
             if ( isUniqueHeaderLine(line, hInfo) )
                 hInfo.add(line);
         }
-        if ( !NO_VCF_HEADER_LINE ) {
-            hInfo.add(new VCFHeaderLine("VariantAnnotator", "\"" + CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), this) + "\""));
-        }
 
         VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
         vcfWriter.writeHeader(vcfHeader);

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

@@ -72,10 +72,6 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
     @Argument(fullName="maskName", shortName="mask", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']", required=false)
     protected String MASK_NAME = "Mask";
 
-    @Hidden
-    @Argument(fullName = "NO_HEADER", shortName = "NO_HEADER", doc = "Don't output the usual VCF header tag with the command line. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.", required = false)
-    protected Boolean NO_VCF_HEADER_LINE = false;
-
     // JEXL expressions for the filters
     List<VariantContextUtils.JexlVCMatchExp> filterExps;
     List<VariantContextUtils.JexlVCMatchExp> genotypeFilterExps;
@@ -113,10 +109,6 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
             }
         }
 
-        if ( !NO_VCF_HEADER_LINE ) {
-            hInfo.add(new VCFHeaderLine("VariantFiltration", "\"" + CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), this) + "\""));
-        }
-
         writer.writeHeader(new VCFHeader(hInfo, vc.getSampleNames()));
     }
 

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

@@ -71,10 +71,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
     protected String[] annotationClassesToUse = { "Standard" };
 
-    @Argument(fullName = "NO_HEADER", shortName = "NO_HEADER", doc = "Don't output the usual VCF header tag with the command line. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.", required = false)
-    protected Boolean NO_VCF_HEADER_LINE = false;
-
-
     // the calculation arguments
     private UnifiedGenotyperEngine UG_engine = null;
 
@@ -154,11 +150,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
              UAC.TRIGGER_CONFIDENCE_FOR_EMITTING < UAC.TRIGGER_CONFIDENCE_FOR_CALLING )
             headerInfo.add(new VCFFilterHeaderLine(UnifiedGenotyperEngine.LOW_QUAL_FILTER_NAME, "Low quality"));
 
-        // all of the arguments from the argument collection
-        if ( !NO_VCF_HEADER_LINE ) {
-            headerInfo.add(new VCFHeaderLine("UnifiedGenotyper", "\"" + CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), this) + "\""));
-        }
-        
         return headerInfo;
     }
 

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

@@ -73,13 +73,6 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
     @Argument(fullName="fdr_filter_level", shortName="fdr_filter_level", doc="The FDR level at which to start filtering.", required=false)
     private double FDR_FILTER_LEVEL = 0.0;
     
-    /////////////////////////////
-    // Debug Arguments
-    /////////////////////////////
-    @Hidden
-    @Argument(fullName = "NO_HEADER", shortName = "NO_HEADER", doc = "Don't output the usual VCF header tag with the command line. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.", required = false)
-    protected Boolean NO_VCF_HEADER_LINE = false;
-    
     /////////////////////////////
     // Private Member Variables
     /////////////////////////////
@@ -167,9 +160,6 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
         // setup the header fields
         final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
-        if( !NO_VCF_HEADER_LINE ) {
-            hInfo.add(new VCFHeaderLine("ApplyVariantCuts", "\"" + CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), this) + "\""));
-        }
         final TreeSet<String> samples = new TreeSet<String>();
         samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit()));
 

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

@@ -111,9 +111,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     // Debug Arguments
     /////////////////////////////
     @Hidden
-    @Argument(fullName = "NO_HEADER", shortName = "NO_HEADER", doc = "Don't output the usual VCF header tag with the command line. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.", required = false)
-    protected Boolean NO_VCF_HEADER_LINE = false;
-    @Hidden
     @Argument(fullName = "NoByHapMapValidationStatus", shortName = "NoByHapMapValidationStatus", doc = "Don't consider sites in dbsnp rod tagged as by-hapmap validation status as real HapMap sites. FOR DEBUGGING PURPOSES ONLY.", required=false)
     private Boolean NO_BY_HAPMAP_VALIDATION_STATUS = false;
 
@@ -182,9 +179,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
         hInfo.add(new VCFInfoHeaderLine("OQ", 1, VCFHeaderLineType.Float, "The original variant quality score"));
         hInfo.add(new VCFInfoHeaderLine("LOD", 1, VCFHeaderLineType.Float, "The log odds ratio calculated by the VR algorithm which was turned into the phred scaled recalibrated quality score"));
-        if( !NO_VCF_HEADER_LINE ) {
-            hInfo.add(new VCFHeaderLine("VariantRecalibrator", "\"" + CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), this) + "\""));
-        }
         samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));
 
         final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);

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

@@ -81,10 +81,6 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="setKey", shortName="setKey", doc="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from.  Set to null if you don't want the set field emitted.", required=false)
     public String SET_KEY = "set";
 
-    @Hidden
-    @Argument(fullName = "NO_HEADER", shortName = "NO_HEADER", doc = "Don't output the usual VCF header tag with the command line. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.", required = false)
-    protected Boolean NO_VCF_HEADER_LINE = false;
-
     private List<String> priority = null;
 
     private VariantAnnotatorEngine engine;
@@ -105,9 +101,6 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger);
         if ( SET_KEY != null )
             headerLines.add(new VCFInfoHeaderLine(SET_KEY, 1, VCFHeaderLineType.String, "Source VCF for the merged record in CombineVariants"));
-        if ( !NO_VCF_HEADER_LINE ) {
-            headerLines.add(new VCFHeaderLine("CombineVariants", "\"" + CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), this) + "\""));
-        }
         vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
     }
 

java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java

@@ -83,7 +83,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
     @Override
     protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() {
         List<ArgumentTypeDescriptor> typeDescriptors = new ArrayList<ArgumentTypeDescriptor>();
-        typeDescriptors.add(new VCFWriterArgumentTypeDescriptor(GATKEngine,System.out));
+        typeDescriptors.add(new VCFWriterArgumentTypeDescriptor(GATKEngine,System.out,Collections.<Object>emptyList()));
         typeDescriptors.add(new SAMFileReaderArgumentTypeDescriptor(GATKEngine));
         typeDescriptors.add(new SAMFileWriterArgumentTypeDescriptor(GATKEngine,System.out));
         typeDescriptors.add(new OutputStreamArgumentTypeDescriptor(GATKEngine,System.out));

java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java

@@ -31,6 +31,7 @@ import java.lang.reflect.Modifier;
 import java.lang.reflect.Field;
 import java.io.File;
 import java.io.IOException;
+import java.util.Collection;
 import java.util.List;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -146,4 +147,35 @@ public class JVMUtils {
         }
     }
 
+    /**
+     * Gets a single object in the list matching or type-compatible with the given type.  Exceptions out if multiple objects match. 
+     * @param type The desired type.
+     * @param <T> The selected type.
+     * @return A collection of the given arguments with the specified type.
+     */
+    public static <T> T getObjectOfType(Collection<Object> objectsToFilter, Class<T> type) {
+        // TODO: Make JVM utils.
+        Collection<T> selectedObjects = getObjectsOfType(objectsToFilter,type);
+        if(selectedObjects.size() > 1)
+            throw new ReviewedStingException("User asked for a single instance of the type, multiple were present");
+        if(selectedObjects.size() == 0)
+            throw new ReviewedStingException("User asked for a single instance of the type, but none were present");
+        return selectedObjects.iterator().next();
+    }
+
+    /**
+     * Gets a collection of all objects in the list matching or type-compatible with the given type. 
+     * @param type The desired type.
+     * @param <T> Again, the desired type.  Used so that clients can ignore type safety.
+     * @return A collection of the given arguments with the specified type.
+     */
+    public static <T> Collection<T> getObjectsOfType(Collection<Object> objectsToFilter, Class<T> type) {
+        Collection<T> selectedObjects = new ArrayList<T>();
+        for(Object object: objectsToFilter) {
+            if(type.isAssignableFrom(object.getClass()))
+                selectedObjects.add((T)object);
+        }
+        return selectedObjects;
+    }
+
 }

java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java

@@ -62,8 +62,6 @@ public class PackageUtils {
      * Private constructor.  No instantiating this class!
      */
     private PackageUtils() {}
-    {
-    }
 
     /**
      * Return the classes that implement the specified interface.

java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java

@@ -28,7 +28,8 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
                         " -T VariantsToVCF" +
                         " -L 1:10,000,000-11,000,000" +
                         " -sample NA123AB" +
-                        " -o %s",
+                        " -o %s" +
+                        " -NO_HEADER",
                 1, // just one output file
                 md5);
         executeTest("testVariantsToVCFUsingGeliInput #1", spec).getFirst();
@@ -45,7 +46,8 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
                         " -T VariantsToVCF" +
                         " -L 1:10,000,000-11,000,000" +
                         " -sample NA123AB" +
-                        " -o %s",
+                        " -o %s" +
+                        " -NO_HEADER",
                 1, // just one output file
                 md5);
         executeTest("testVariantsToVCFUsingGeliInput #2", spec).getFirst();
@@ -61,7 +63,8 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
                         " -B:variant,HapMap " + validationDataLocation + "rawHapMap.yri.chr1.txt" +
                         " -T VariantsToVCF" +
                         " -L 1:1-1,000,000" +
-                        " -o %s",
+                        " -o %s" +
+                        " -NO_HEADER",
                 1, // just one output file
                 md5);
         executeTest("testVariantsToVCFUsingHapMapInput", spec).getFirst();
@@ -76,7 +79,8 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
                 "-R " + b36KGReference +
                         " -B:variant,VCF " + validationDataLocation + "complexExample.vcf4" +
                         " -T VariantsToVCF" +
-                        " -o %s",
+                        " -o %s" +
+                        " -NO_HEADER",
                 1, // just one output file
                 md5);
         executeTest("testVariantsToVCFUsingVCFInput", spec).getFirst();

java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java

@@ -6,7 +6,8 @@ import java.util.Arrays;
 import org.broadinstitute.sting.WalkerTest;
 import org.junit.Test;
 
-public class GenomicAnnotatorIntegrationTest extends WalkerTest {
+public class
+        GenomicAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testGenomicAnnotatorOnDbSNP() {
 
@@ -34,7 +35,8 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
                 " -m" + //generate many records from one input record if necessary
                 " -o %s" +
                 " -BTI variant" +
-                " -s dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet",
+                " -s dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet" +
+                " -NO_HEADER",
                  1,
                  Arrays.asList(md5WithDashSArg));
         executeTest("test with dbSNP and -s arg", specWithSArg);

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -11,7 +11,8 @@ import java.util.Map;
 // Note that this class also serves as an integration test for the VariantAnnotator!  //
 // ********************************************************************************** //
 
-public class UnifiedGenotyperIntegrationTest extends WalkerTest {
+public class
+        UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER";
 

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java

@@ -38,7 +38,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
     @Test
     public void testb36Tohg19() {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
+                 "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict -NO_HEADER",
                  1,
                  Arrays.asList("1637877892a019061e74eb3d9a9d100f"));
          executeTest("test b36 to hg19", spec);

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -16,7 +16,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
 
         WalkerTestSpec spec = new WalkerTestSpec(
-            baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'AF < 0.2' -B:variant,VCF " + testfile),
+            baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'AF < 0.2' -B:variant,VCF " + testfile + " -NO_HEADER"),
             1,
             Arrays.asList("3a15628b5980031c629c0c33e7e60b40")
         );