RodBinding subclassed to VariantContextRodBinding for easy access to VariantContext providing RODs

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

@@ -291,17 +291,28 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     }
 
     public static boolean isRodBinding( Class type ) {
-        return type.isAssignableFrom(RodBinding.class);
+        return RodBinding.class.isAssignableFrom(type);
     }
 
     @Override
     public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches) {
         ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
         String value = getArgumentValue( defaultDefinition, matches );
-        RodBinding<Object> result = new RodBinding<Object>(source.field.getName(), new File(value));
+        try {
+            Constructor ctor = type.getConstructor(String.class, String.class);
+            RodBinding result = (RodBinding)ctor.newInstance(source.field.getName(), value);
             Tags tags = getArgumentTags(matches);
             parsingEngine.addTags(result,tags);
             return result;
+        } catch (InvocationTargetException e) {
+            throw new UserException.CommandLineException(
+                    String.format("Failed to parse value %s for argument %s.",
+                            value, source.field.getName()));
+        } catch (Exception e) {
+            throw new UserException.CommandLineException(
+                    String.format("Failed to parse value %s for argument %s.",
+                            value, source.field.getName()));
+        }
     }
 }
 

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

@@ -24,23 +24,18 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.File;
 import java.util.List;
 
 /**
  *
  */
-// TODO -- should have a derived class called VariantContentRodBinding with simple accessors
 public class RodBinding {
     final String variableName;
-    final File sourceFile;
+    final String sourceFile;
 
-    public RodBinding(final String variableName, final File sourceFile) {
+    public RodBinding(final String variableName, final String sourceFile) {
         this.variableName = variableName;
         this.sourceFile = sourceFile;
     }
@@ -49,7 +44,7 @@ public class RodBinding {
         return variableName;
     }
 
-    public File getSourceFile() {
+    public String getSourceFile() {
         return sourceFile;
     }
 
@@ -57,10 +52,6 @@ public class RodBinding {
         return tracker.getReferenceMetaData(variableName);
     }
 
-    public VariantContext getVariantContext(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc) {
-        return tracker.getVariantContext(ref, variableName, loc);
-    }
-
     public String toString() {
         return String.format("(RodBinding name=%s source=%s)", variableName, sourceFile);
     }

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

@@ -0,0 +1,46 @@
+/*
+ * Copyright (c) 2011, 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.commandline;
+
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.File;
+import java.util.List;
+
+/**
+ *
+ */
+public class VariantContextRodBinding extends RodBinding {
+    public VariantContextRodBinding(final String variableName, final String sourceFile) {
+        super(variableName, sourceFile);
+    }
+
+    public VariantContext getVariantContext(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc) {
+        return tracker.getVariantContext(ref, variableName, loc);
+    }
+}

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableNewRodStyle.java

@@ -24,14 +24,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
 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.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.Utils;
@@ -66,9 +62,9 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
     public boolean ALLOW_MISSING_DATA = false;
 
     @Input(fullName="variants", shortName="V", doc="The variant file we will convert to a table", required=true)
-    public RodBinding variants;
+    public VariantContextRodBinding variants;
 
-    @Input(fullName="variantsList", shortName="VL", doc="The variant file we will convert to a table", required=true)
+    @Input(fullName="rodList", shortName="RL", doc="A list of ROD types that we will convert to a table", required=true)
     public List<RodBinding> variantsList;
 
     public void initialize() {
@@ -139,7 +135,7 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
             return 0;
 
         for ( RodBinding binding : variantsList )
-            System.out.printf("VariantList binding %s%n", binding);
+            System.out.printf("VariantList binding %s tags=%s%n", binding, getToolkit().getTags(binding).getPositionalTags());
 
         if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
             VariantContext vc = variants.getVariantContext(tracker, ref, context.getLocation());