Alternative dependency injection issue workaround.

Author: cmnbroad

src/test/java/org/broadinstitute/hellbender/tools/AbstractPrintReadsIntegrationTest.java

@@ -22,11 +22,13 @@
 import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
 import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
 import org.broadinstitute.hellbender.testutils.SamAssertionUtils;
+import org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 import org.testng.Assert;
+import org.testng.SkipException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -75,6 +77,9 @@ public void doFileToFile(String fileIn, String extOut, String reference, boolean
     }
 
     public void doFileToFileUsingReferenceBundle(final String fileIn, final String extOut, final String reference, final boolean testMD5) throws Exception {
+        if (this.getClass().equals(PrintReadsSparkIntegrationTest.class)) {
+            throw new SkipException("Bundles are not supported in Spark tools");
+        }
         final String referenceToUse;
         if (reference != null) {
             // create the bundle, using inference to find the sibling files, then write the bundle out to a temp file

src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java

@@ -31,11 +31,6 @@
 @Test(groups = "spark")
 public final class PrintReadsSparkIntegrationTest extends AbstractPrintReadsIntegrationTest {
 
-    @Override
-    public void doFileToFileUsingReferenceBundle(final String fileIn, final String extOut, final String reference, final boolean testMD5) throws Exception {
-        throw new SkipException("Bundles are not supported in Spark tools");
-    }
-
     @Test()
     public void testUnSortedRoundTrip() throws Exception {
         // This is a technically incorrectly sam with a header indicating that it is coordinate sorted when it is actually