Support reference bundles.

Author: cmnbroad

src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java

@@ -56,10 +56,10 @@ private StandardArgumentDefinitions(){}
     public static final String INTERVALS_SHORT_NAME = "L";
     public static final String COMPARISON_SHORT_NAME = "comp";
     public static final String READ_INDEX_SHORT_NAME = READ_INDEX_LONG_NAME;
-    public static final String PRIMARY_INPUT_LONG_NAME = "primary";
-    public static final String PRIMARY_INPUT_SHORT_NAME = "PI";
-    public static final String SECONDARY_INPUT_LONG_NAME = "secondaryI";
-    public static final String SECONDARY_INPUT_SHORT_NAME = "SI";
+    public static final String PRIMARY_RESOURCE_LONG_NAME = "primary-resource";
+    public static final String PRIMARY_RESOURCE_SHORT_NAME = "PR";
+    public static final String SECONDARY_RESOURCE_LONG_NAME = "secondary-resource";
+    public static final String SECONDARY_RESOURCE_SHORT_NAME = "SR";
     public static final String LENIENT_SHORT_NAME = "LE";
     public static final String READ_VALIDATION_STRINGENCY_SHORT_NAME = "VS";
     public static final String SAMPLE_ALIAS_SHORT_NAME = "ALIAS";

src/main/java/org/broadinstitute/hellbender/engine/FeatureInput.java

@@ -54,7 +54,8 @@ public final class FeatureInput<T extends Feature> extends GATKPath implements S
     private transient Class<FeatureCodec<T, ?>> featureCodecClass;
 
     /**
-     * retain any containing bundle in case we need to extract other resources from it
+     * retain the parent (enclosing) bundle from which this feature input is derived, in case we need to extract
+     * other resources from it
      */
     private Bundle parentBundle;
 
@@ -148,7 +149,7 @@ public FeatureInput(
             final Bundle featureBundle,
             final String name) {
         super(primaryResourcePath);
-        // retain the containing bundle for later so we can interrogate it for other resources, like the index
+        // retain the enclosing bundle for later, so we can interrogate it for other resources such as the index
         this.parentBundle = featureBundle;
         if (name != null) {
             if (primaryResourcePath.getTag() != null) {

src/main/java/org/broadinstitute/hellbender/engine/MultiVariantWalker.java

@@ -86,15 +86,17 @@ protected void initializeDrivingVariants() {
                         final List<Bundle> bundles = BundleJSON.toBundleList(IOUtils.getStringFromPath(gatkPath), GATKPath::new);
                         for (final Bundle bundle : bundles) {
                             if (bundle.getPrimaryContentType().equals(BundleResourceType.CT_VARIANT_CONTEXTS)) {
-                                // use the bundle primary resource as the FeatureInput URI, and tear off and attach the
-                                // individual bundle the bundle to the FI as the parent bundle so downstream code can
-                                // extract other resources from it on demand
-                                // note that if the original value from the user has a tag, we can't use it unless there
-                                // is only one input, since FIs have to be unique
+                                // use the bundle primary resource as the FeatureInput URI, and tear off and attach
+                                // the enclosing bundle as the parent bundle for the FI so downstream code can extract
+                                // other resources from it on demand. note that if the original value from the user has
+                                // a tag, we can't propagate it unless there is only one input, since FIs have to be
+                                // unique
                                 final FeatureInput<VariantContext> bundleFI = new FeatureInput<>(
                                         new GATKPath(bundle.getPrimaryResource().getIOPath().get().getURIString()),
                                         bundle,
-                                        bundles.size() > 1 ? gatkPath.getTag() : "drivingVariants"
+                                        bundles.size() > 1 ?
+                                                gatkPath.getTag() :
+                                                "drivingVariants"
                                 );
                                 if (drivingVariantsFeatureInputs.contains(bundleFI)) {
                                     throw new UserException.BadInput("Feature inputs must be unique: " + gatkPath);