Item #1 -- remove instanceof call and let every GATKTool have default

GenomicsDB options
broadinstitute · Aug 2, 2019 · c41b05d · c41b05d
1 parent 5fd4d9b
commit c41b05d
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java b/src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java
@@ -147,14 +147,14 @@ public FeatureManager(final CommandLineProgram toolInstance, final int featureQu
      *                              the end of query intervals in anticipation of future queries (>= 0).
      * @param cloudPrefetchBuffer MB size of caching/prefetching wrapper for the data, if on Google Cloud (0 to disable).
      * @param cloudIndexPrefetchBuffer MB size of caching/prefetching wrapper for the index, if on Google Cloud (0 to disable).
-     * @param reference reference to use when opening feature files, may be null, currently only used by Genomics DB
+     * @param gdbOptions settings for GenomicsDB to use when reading from a GenomicsDB workspace
      *
      */
-    public FeatureManager(final CommandLineProgram toolInstance, final int featureQueryLookahead, final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final Path reference) {
+    public FeatureManager(final CommandLineProgram toolInstance, final int featureQueryLookahead, final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final GenomicsDBOptions gdbOptions) {
         this.toolInstanceSimpleClassName = toolInstance.getClass().getSimpleName();
         this.featureSources = new LinkedHashMap<>();
 
-        initializeFeatureSources(featureQueryLookahead, toolInstance, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, reference);
+        initializeFeatureSources(featureQueryLookahead, toolInstance, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, gdbOptions);
     }
 
     /**
@@ -193,7 +193,7 @@ public FeatureManager(final CommandLineProgram toolInstance, final int featureQu
      * @param cloudIndexPrefetchBuffer MB size of caching/prefetching wrapper for the index, if on Google Cloud (0 to disable).
      */
     @SuppressWarnings({"unchecked", "rawtypes"})
-    private void initializeFeatureSources( final int featureQueryLookahead, final CommandLineProgram toolInstance, final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final Path reference) {
+    private void initializeFeatureSources( final int featureQueryLookahead, final CommandLineProgram toolInstance, final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final GenomicsDBOptions gdbOptions) {
 
         // Discover all arguments of type FeatureInput (or Collections thereof) in our tool's class hierarchy
         // (and associated ArgumentCollections). Arguments not specified by the user on the command line will
@@ -208,7 +208,7 @@ private void initializeFeatureSources( final int featureQueryLookahead, final Co
             if ( featureInput != null ) {
                 final Class<? extends Feature> featureType = getFeatureTypeForFeatureInputField(featureArgument.getKey());
                 addToFeatureSources(featureQueryLookahead, featureInput, featureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer,
-                        toolInstance instanceof VariantWalker ? ((VariantWalker) toolInstance).getGenomicsDBOptions() : null);
+                        gdbOptions);
             }
         }
     }

diff --git a/src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java b/src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java
@@ -415,11 +415,11 @@ protected List<SimpleInterval> transformTraversalIntervals(final List<SimpleInte
     }
 
     /**
-     *
-     * @return By default, not every GATK tool can read from a GenomicsDB -- child classes can override
+     * Get the GenomicsDB read settings for the current tool
+     * @return By default, just return the vanilla options
      */
     protected GenomicsDBOptions getGenomicsDBOptions() {
-        throw new IllegalArgumentException("This tool does not take a GenomicsDB as a feature input.");
+        return new GenomicsDBOptions(referenceArguments.getReferencePath());
     }
 
     /**
@@ -481,8 +481,8 @@ private boolean hasCramInput() {
      * By default, this method initializes the FeatureManager to use the lookahead cache of {@link FeatureDataSource#DEFAULT_QUERY_LOOKAHEAD_BASES} bases.
      */
     void initializeFeatures() {
-        features = new FeatureManager(this, FeatureDataSource.DEFAULT_QUERY_LOOKAHEAD_BASES, cloudPrefetchBuffer, cloudIndexPrefetchBuffer,
-                                      referenceArguments.getReferencePath());
+        features = new FeatureManager(this, FeatureDataSource.DEFAULT_QUERY_LOOKAHEAD_BASES, cloudPrefetchBuffer,
+                cloudIndexPrefetchBuffer, getGenomicsDBOptions());
         if ( features.isEmpty() ) {  // No available sources of Features discovered for this tool
             features = null;
         }