Update my code for GDB protobuf update

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

@@ -253,6 +253,7 @@ public FeatureDataSource(final FeatureInput<T> featureInput, final int queryLook
      * @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 Path to a reference. May be null. Needed only for reading from GenomicsDB.
+     * @param doGnarlyGenotyping indicates whether the GenomicsDB export configuration should be modified for the GnarlyGenotyper
      */
     public FeatureDataSource(final FeatureInput<T> featureInput, final int queryLookaheadBases, final Class<? extends Feature> targetFeatureType,
                              final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final Path reference, final boolean doGnarlyGenotyping) {

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

@@ -179,11 +179,18 @@ private void initializeFeatureSources( final int featureQueryLookahead, final Co
             // Only create a data source for Feature arguments that were actually specified
             if ( featureInput != null ) {
                 final Class<? extends Feature> featureType = getFeatureTypeForFeatureInputField(featureArgument.getKey());
-                addToFeatureSources(featureQueryLookahead, featureInput, featureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, reference);
+                addToFeatureSources(featureQueryLookahead, featureInput, featureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, reference, false);
             }
         }
     }
 
+    void addToFeatureSources(final int featureQueryLookahead, final FeatureInput<? extends Feature> featureInput,
+                             final Class<? extends Feature> featureType, final int cloudPrefetchBuffer,
+                             final int cloudIndexPrefetchBuffer, final Path reference) {
+        // Create a new FeatureDataSource for this file, and add it to our query pool
+        featureSources.put(featureInput, new FeatureDataSource<>(featureInput, featureQueryLookahead, featureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, reference, false));
+    }
+
 
     /**
      * Add the feature data source to the given feature input.
@@ -193,13 +200,16 @@ private void initializeFeatureSources( final int featureQueryLookahead, final Co
      * @param featureType class of features
      * @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 doGnarlyGenotyping indicates whether the GenomicsDB export configuration should be modified for the GnarlyGenotyper
      *
      * Note: package-visible to enable access from the core walker classes
      * (but not actual tools, so it's not protected).
      */
-    void addToFeatureSources(final int featureQueryLookahead, final FeatureInput<? extends Feature> featureInput, final Class<? extends Feature> featureType, final int cloudPrefetchBuffer, final int cloudIndexPrefetchBuffer, final Path reference) {
+    void addToFeatureSources(final int featureQueryLookahead, final FeatureInput<? extends Feature> featureInput,
+                             final Class<? extends Feature> featureType, final int cloudPrefetchBuffer,
+                             final int cloudIndexPrefetchBuffer, final Path reference, final boolean doGnarlyGenotyping) {
         // Create a new FeatureDataSource for this file, and add it to our query pool
-        featureSources.put(featureInput, new FeatureDataSource<>(featureInput, featureQueryLookahead, featureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, reference));
+        featureSources.put(featureInput, new FeatureDataSource<>(featureInput, featureQueryLookahead, featureType, cloudPrefetchBuffer, cloudIndexPrefetchBuffer, reference, doGnarlyGenotyping));
     }
 
     /**

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

@@ -58,7 +58,7 @@ protected void initializeDrivingVariants() {
         //Add the driving datasource to the feature manager too so that it can be queried. Setting lookahead to 0 to avoid caching.
         //Note: we are disabling lookahead here because of windowed queries that need to "look behind" as well.
         features.addToFeatureSources(0, drivingVariantsFeatureInput, VariantContext.class, cloudPrefetchBuffer, cloudIndexPrefetchBuffer,
-                                     referenceArguments.getReferencePath());
+                                     referenceArguments.getReferencePath(), doGenotypeCalling());
 
         //Note: the intervals for the driving variants are set in onStartup
     }

src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java

@@ -53,28 +53,6 @@ public class GnarlyGenotyperIntegrationTest extends CommandLineProgramTest {
 
 
 
-    private static String getQueryJsonForGenomicsDB(String vidMappingFile, String callsetMappingFile, String tiledbWorkspace,
-                                                    String referenceGenome) throws IOException {
-        //Produce temporary JSON query config file
-        String indentString = "    ";
-        String queryJSON = "{\n";
-        queryJSON += indentString + "\"scan_full\": true,\n";
-        queryJSON += indentString + "\"workspace\": \""+tiledbWorkspace+"\",\n";
-        queryJSON += indentString + "\"array\": \""+GenomicsDBConstants.DEFAULT_ARRAY_NAME+"\",\n";
-        queryJSON += indentString + "\"vid_mapping_file\": \""+vidMappingFile+"\",\n";
-        queryJSON += indentString + "\"callset_mapping_file\": \""+callsetMappingFile+"\",\n";
-        queryJSON += indentString + "\"produce_GT_field\": true,\n";
-        queryJSON += indentString + "\"max_diploid_alt_alleles_that_can_be_genotyped\": 6,\n";
-        queryJSON += indentString + "\"reference_genome\": \""+referenceGenome+"\"";
-        queryJSON += "\n}\n";
-        File tmpQueryJSONFile = new File(tiledbWorkspace, "query.json");
-        tmpQueryJSONFile.deleteOnExit();
-        FileWriter fptr = new FileWriter(tmpQueryJSONFile);
-        fptr.write(queryJSON);
-        fptr.close();
-        return tmpQueryJSONFile.getAbsolutePath();
-    }
-
     @DataProvider(name="VCFdata")
     public Object[][] getVCFdata() {
         return new Object[][]{
@@ -92,10 +70,6 @@ public void testUsingGenomicsDB(File[] inputs, File expected, String interval, L
 
         //copy in the extra files until Protobuf update in PR #4645 is ready
         Runtime.getRuntime().exec("cp " + getTestFile("vidmap.updated.json").getAbsolutePath() +" "+ tempGenomicsDB.getAbsolutePath() + "/vidmap.json");
-        getQueryJsonForGenomicsDB(new File(tempGenomicsDB, GenomicsDBConstants.DEFAULT_VIDMAP_FILE_NAME).getAbsolutePath(),
-                new File(tempGenomicsDB, GenomicsDBConstants.DEFAULT_CALLSETMAP_FILE_NAME).getAbsolutePath(),
-                tempGenomicsDB.getAbsolutePath(),
-                reference);
 
         File output = runTool(genomicsDBUri, interval, reference, additionalArguments);