Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

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

@@ -185,7 +185,7 @@ public class ArgumentSource {
      * @return A default value for the given type.
      */
     public Object createTypeDefault(ParsingEngine parsingEngine) {
-        return typeDescriptor.createTypeDefault(parsingEngine,this,field.getType());
+        return typeDescriptor.createTypeDefault(parsingEngine,this,field.getGenericType());
     }
 
     /**

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

@@ -96,12 +96,13 @@ public abstract class ArgumentTypeDescriptor {
 
     /**
      * Generates a default for the given type.
+     *
      * @param parsingEngine the parsing engine used to validate this argument type descriptor.
      * @param source Source of the command-line argument.
      * @param type Type of value to create, in case the command-line argument system wants influence.
      * @return A default value for the given type.
      */
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) { throw new UnsupportedOperationException("Unable to create default for type " + getClass()); }
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) { throw new UnsupportedOperationException("Unable to create default for type " + getClass()); }
 
     /**
      * Given the given argument source and attributes, synthesize argument definitions for command-line arguments.
@@ -323,8 +324,9 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     public boolean createsTypeDefault(ArgumentSource source) { return ! source.isRequired(); }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine, ArgumentSource source, Class<?> type) {
+    public Object createTypeDefault(ParsingEngine parsingEngine, ArgumentSource source, Type type) {
-        return RodBinding.makeUnbound((Class<? extends Feature>)type);
+        Class parameterType = getParameterizedTypeClass(type);
+        return RodBinding.makeUnbound((Class<? extends Feature>)parameterType);
     }
 
     @Override
@@ -646,7 +648,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) {
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) {
         if(multiplexer == null || multiplexedIds == null)
             throw new ReviewedStingException("No multiplexed ids available");
 

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

@@ -364,7 +364,7 @@ public class ParsingEngine {
      */
     private void loadValueIntoObject( ArgumentSource source, Object instance, ArgumentMatches argumentMatches ) {
         // Nothing to load
-        if( argumentMatches.size() == 0 && !(source.createsTypeDefault() && source.isRequired()))
+        if( argumentMatches.size() == 0 && ! source.createsTypeDefault() )
             return;
 
         // Target instance into which to inject the value.

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

@@ -75,12 +75,12 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class type) {
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) {
         if(!source.isRequired())
             throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default.");
         OutputStreamStub stub = new OutputStreamStub(defaultOutputStream);
         engine.addOutput(stub);
-        return createInstanceOfClass(type,stub);        
+        return createInstanceOfClass((Class)type,stub);
     }
 
     @Override

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

@@ -99,7 +99,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) {
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) {
         if(!source.isRequired())
             throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default.");
         SAMFileWriterStub stub = new SAMFileWriterStub(engine,defaultOutputStream);

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

@@ -114,7 +114,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     @Override
-    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source,Class<?> type) {
+    public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) {
         if(!source.isRequired())
             throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default.");        
         VCFWriterStub stub = new VCFWriterStub(engine, defaultOutputStream, false, argumentSources, false, false);

public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java

@@ -632,8 +632,8 @@ public class ParsingEngineUnitTest extends BaseTest {
     // --------------------------------------------------------------------------------
 
     private class SingleRodBindingArgProvider {
-        @Input(fullName="binding", shortName="V", required=false)
+        @Input(fullName="binding", shortName="V", required=true)
-        public RodBinding<Feature> binding = RodBinding.makeUnbound(Feature.class);
+        public RodBinding<Feature> binding;
     }
 
     @Test
@@ -656,7 +656,7 @@ public class ParsingEngineUnitTest extends BaseTest {
 
     private class ShortNameOnlyRodBindingArgProvider {
         @Input(shortName="short", required=false)
-        public RodBinding<Feature> binding = RodBinding.makeUnbound(Feature.class);
+        public RodBinding<Feature> binding; // = RodBinding.makeUnbound(Feature.class);
     }
 
     @Test
@@ -677,22 +677,38 @@ public class ParsingEngineUnitTest extends BaseTest {
         Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");
     }
 
+    private class OptionalRodBindingArgProvider {
+        @Input(fullName="binding", shortName="V", required=false)
+        public RodBinding<Feature> binding;
+
+        @Input(fullName="bindingNull", shortName="VN", required=false)
+        public RodBinding<VariantContext> bindingNull = null;
+    }
+
     @Test
-    public void unbasicRodBindingArgumentTest() {
+    public void optionalRodBindingArgumentTest() {
         final String[] commandLine = new String[] {};
 
-        parsingEngine.addArgumentSource( SingleRodBindingArgProvider.class );
+        parsingEngine.addArgumentSource( OptionalRodBindingArgProvider.class );
         parsingEngine.parse( commandLine );
         parsingEngine.validate();
 
-        SingleRodBindingArgProvider argProvider = new SingleRodBindingArgProvider();
+        OptionalRodBindingArgProvider argProvider = new OptionalRodBindingArgProvider();
         parsingEngine.loadArgumentsIntoObject( argProvider );
 
+        Assert.assertNotNull(argProvider.binding, "Default value not applied corrected to RodBinding");
         Assert.assertEquals(argProvider.binding.getName(), RodBinding.UNBOUND_VARIABLE_NAME, "Name isn't set properly");
         Assert.assertEquals(argProvider.binding.getSource(), RodBinding.UNBOUND_SOURCE, "Source isn't set to its expected value");
         Assert.assertEquals(argProvider.binding.getType(), Feature.class, "Type isn't set to its expected value");
         Assert.assertEquals(argProvider.binding.isBound(), false, "Bound() isn't returning its expected value");
         Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 0, "Tags aren't correctly set");
+
+        Assert.assertNotNull(argProvider.bindingNull, "Default value not applied corrected to RodBinding");
+        Assert.assertEquals(argProvider.bindingNull.getName(), RodBinding.UNBOUND_VARIABLE_NAME, "Name isn't set properly");
+        Assert.assertEquals(argProvider.bindingNull.getSource(), RodBinding.UNBOUND_SOURCE, "Source isn't set to its expected value");
+        Assert.assertEquals(argProvider.bindingNull.getType(), VariantContext.class, "Type isn't set to its expected value");
+        Assert.assertEquals(argProvider.bindingNull.isBound(), false, "Bound() isn't returning its expected value");
+        Assert.assertEquals(argProvider.bindingNull.getTags().getPositionalTags().size(), 0, "Tags aren't correctly set");
     }
 
     @Test(expectedExceptions = UserException.class)