Attempt to fix dependency injection issue.

Author: cmnbroad

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

@@ -74,7 +74,7 @@ public void doFileToFile(String fileIn, String extOut, String reference, boolean
         }
     }
 
-    public void doFileToFileUsingReferenceBundle(String fileIn, String extOut, String reference, boolean testMD5) throws Exception {
+    public void doFileToFileUsingReferenceBundle(final String fileIn, final String extOut, final String reference, final boolean testMD5) throws Exception {
         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
@@ -148,7 +148,7 @@ public Object[][] testingData() {
     }
 
     @Test(dataProvider="testingData")
-    public void testFileToFileUsingReferenceBundle(String fileIn, String extOut, String reference) throws Exception {
+    public void testFileToFileUsingReferenceBundle(final String fileIn, final String extOut, final String reference) throws Exception {
         if (reference != null) {
             doFileToFileUsingReferenceBundle(fileIn, extOut, reference, false);
         }

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

@@ -160,7 +160,7 @@ public void testPrintReadsWithReferenceBundle() throws IOException {
     // only do reference bundle tests for non-spark tools, since for now the spark tools don't support reference bundles
     // (since they use 2-bit and hadoop references)
     @Test(dataProvider="testingData")
-    public void testFileToFileWithReferenceBundle(String fileIn, String extOut, String reference) throws Exception {
+    public void testFileToFileWithReferenceBundle(final String fileIn, final String extOut, final String reference) throws Exception {
         doFileToFileUsingReferenceBundle(fileIn, extOut, reference, false);
     }
 

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

@@ -32,7 +32,7 @@
 public final class PrintReadsSparkIntegrationTest extends AbstractPrintReadsIntegrationTest {
 
     @Override
-    public void doFileToFileUsingReferenceBundle(String fileIn, String extOut, String reference, boolean testMD5) throws Exception {
+    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");
     }