UnifiedGenotyper now works without -varout or -vf set.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2464 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -58,6 +58,26 @@ public class GenotypeWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
                               createGenotypeFormatArgumentDefinition(source) );
     }
 
+    /**
+     * This command-line argument descriptor does want to override the provided default value.
+     * @return true always.
+     */
+    @Override
+    public boolean overridesDefault() {
+        return true;
+    }
+
+    /**
+     * Provide the default value for this argument.
+     * @return A VCFGenotypeWriter which writes to the default output stream.
+     */
+    @Override
+    public Object getDefault() {
+        GenotypeWriterStub defaultGenotypeWriter = new VCFGenotypeWriterStub(engine,System.out);
+        engine.addOutput(defaultGenotypeWriter);
+        return defaultGenotypeWriter;       
+    }
+
     /**
      * Convert the given argument matches into a single object suitable for feeding into the ArgumentSource.
      * @param source Source for this argument.

java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentSource.java

@@ -48,6 +48,11 @@ public class ArgumentSource {
      */
     public final Field field;
 
+    /**
+     * Type descriptor to use when parsing new argument types.
+     */
+    private final ArgumentTypeDescriptor typeDescriptor;
+
     /**
      * Create a new command-line argument target.
      * @param clazz Class containing the argument.
@@ -56,6 +61,7 @@ public class ArgumentSource {
     public ArgumentSource( Class clazz, Field field ) {
         this.clazz = clazz;
         this.field = field;
+        this.typeDescriptor = ArgumentTypeDescriptor.create( field.getType() );
     }
 
     /**
@@ -89,10 +95,25 @@ public class ArgumentSource {
      * @return A non-null, non-empty list of argument definitions.
      */
     public List<ArgumentDefinition> createArgumentDefinitions() {
-        ArgumentTypeDescriptor typeDescriptor = ArgumentTypeDescriptor.create( field.getType() );
         return typeDescriptor.createArgumentDefinitions( this );
     }
 
+    /**
+     * This argument type descriptor wants to override any default value the user might have specified.
+     * @return True if this descriptor wants to override any default the user specified.  False otherwise.
+     */
+    public boolean overridesDefault() {
+        return typeDescriptor.overridesDefault();
+    }
+
+    /**
+     * Provides the default value for the command-line argument.
+     * @return Default value to load into the object.
+     */
+    public Object getDefault() {
+        return typeDescriptor.getDefault();
+    }
+
     /**
      * Parses the specified value based on the specified type.
      * @param source The type of value to be parsed.
@@ -101,10 +122,8 @@ public class ArgumentSource {
      */
     public Object parse( ArgumentSource source, ArgumentMatches values ) {
         Object value = null;
-        if( !isFlag() ) {
+        if( !isFlag() )
-            ArgumentTypeDescriptor typeDescriptor = ArgumentTypeDescriptor.create( field.getType() );
             value = typeDescriptor.parse( source, values );
-        }
         else
             value = true;
 

java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java

@@ -65,6 +65,11 @@ public abstract class ArgumentTypeDescriptor {
         descriptors = allDescriptors;
     }
 
+    /**
+     * Fetch the given descriptor from the descriptor repository.
+     * @param type Class for which to specify a descriptor.
+     * @return descriptor for the given type.
+     */
     public static ArgumentTypeDescriptor create( Class type ) {
         for( ArgumentTypeDescriptor descriptor: descriptors ) {
             if( descriptor.supports(type) )
@@ -80,6 +85,22 @@ 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. 
+     * @return True if this descriptor wants to override any default the user specified.  False otherwise.
+     */
+    public boolean overridesDefault() {
+        return false;
+    }
+
+    /**
+     * Provides the default value for the command-line argument.
+     * @return Default value to load into the object.
+     */
+    public Object getDefault() {
+        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.
      * @param source Source class and field for the given argument.
@@ -115,6 +136,7 @@ public abstract class ArgumentTypeDescriptor {
     /**
      * Retrieves the full name of the argument, specifiable with the '--' prefix.  The full name can be
      * either specified explicitly with the fullName annotation parameter or implied by the field name.
+     * @param source Original field specifying command-line arguments.
      * @return full name of the argument.  Never null.
      */
     protected String getFullName( ArgumentSource source ) {
@@ -125,6 +147,7 @@ public abstract class ArgumentTypeDescriptor {
     /**
      * Retrieves the short name of the argument, specifiable with the '-' prefix.  The short name can
      * be specified or not; if left unspecified, no short name will be present.
+     * @param source Original field specifying command-line arguments.
      * @return short name of the argument.  Null if no short name exists.
      */
     protected String getShortName( ArgumentSource source ) {
@@ -134,6 +157,7 @@ public abstract class ArgumentTypeDescriptor {
 
     /**
      * Documentation for this argument.  Mandatory field.
+     * @param source Original field specifying command-line arguments.
      * @return Documentation for this argument.
      */
     protected String getDoc( ArgumentSource source ) {
@@ -143,6 +167,7 @@ public abstract class ArgumentTypeDescriptor {
 
     /**
      * Returns whether this field is required.  Note that flag fields are always forced to 'not required'.
+     * @param source Original field specifying command-line arguments.
      * @return True if the field is mandatory and not a boolean flag.  False otherwise.
      */
     protected boolean isRequired( ArgumentSource source ) {
@@ -152,6 +177,7 @@ public abstract class ArgumentTypeDescriptor {
 
     /**
      * Specifies other arguments which cannot be used in conjunction with tihs argument.  Comma-separated list.
+     * @param source Original field specifying command-line arguments.
      * @return A comma-separated list of exclusive arguments, or null if none are present.
      */
     protected String getExclusiveOf( ArgumentSource source ) {
@@ -161,6 +187,7 @@ public abstract class ArgumentTypeDescriptor {
 
     /**
      * A regular expression which can be used for validation.
+     * @param source Original field specifying command-line arguments.
      * @return a JVM regex-compatible regular expression, or null to permit any possible value.
      */
     protected String getValidationRegex( ArgumentSource source ) {

java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java

@@ -250,7 +250,7 @@ public class ParsingEngine {
     public void loadArgumentsIntoObject( Object object ) {
         List<ArgumentSource> argumentSources = extractArgumentSources(object.getClass());
         for( ArgumentSource argumentSource: argumentSources )
-            loadMatchesIntoObject( argumentSource, object, argumentMatches.findMatches(argumentSource) );
+            loadValueIntoObject( argumentSource, object, argumentMatches.findMatches(argumentSource) );
     }
 
     /**
@@ -259,9 +259,9 @@ public class ParsingEngine {
      * @param source Argument source to load into the object.
      * @param instance Object into which to inject the value.  The target might be in a container within the instance.
      */
-    private void loadMatchesIntoObject( ArgumentSource source, Object instance, ArgumentMatches argumentMatches ) {
+    private void loadValueIntoObject( ArgumentSource source, Object instance, ArgumentMatches argumentMatches ) {
         // Nothing to load
-        if( argumentMatches.size() == 0 )
+        if( argumentMatches.size() == 0 && !source.overridesDefault())
             return;
 
         // Target instance into which to inject the value.
@@ -280,7 +280,7 @@ 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 = source.parse( source, argumentMatches );
+            Object value = (argumentMatches.size() != 0) ? source.parse(source,argumentMatches) : source.getDefault();
             JVMUtils.setFieldValue(source.field,target,value);
         }
     }