Suppress more deprecation warnings.

src/main/java/org/broadinstitute/hellbender/tools/dragstr/CalibrateDragstrModel.java

@@ -263,6 +263,7 @@ private void checkSequenceDictionaryCompatibility(final SAMSequenceDictionary re
         }
     }
 
+    @SuppressWarnings("deprecation")
     private PrintWriter openSitesOutputWriter(final String sitesOutput) {
         return sitesOutput == null ? new PrintWriter(new NullOutputStream())
                 : new PrintWriter(BucketUtils.createFile(sitesOutput));

src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKAnnotationPluginDescriptorUnitTest.java

@@ -36,6 +36,7 @@
 
 public class GATKAnnotationPluginDescriptorUnitTest extends GATKBaseTest {
     // null print stream for the tests
+    @SuppressWarnings("deprecation")
     private static final PrintStream nullMessageStream = new PrintStream(new NullOutputStream());
 
 //======================================================================================================================

src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKReadFilterPluginDescriptorTest.java

@@ -35,6 +35,7 @@
 public class GATKReadFilterPluginDescriptorTest extends GATKBaseTest {
 
     // null print stream for the tests
+    @SuppressWarnings("deprecation")
     private static final PrintStream nullMessageStream = new PrintStream(new NullOutputStream());
 
     @DataProvider(name = "defaultFiltersForAllowedValues")

src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java

@@ -633,6 +633,7 @@ public static VCFHeader getCompleteHeader() {
     /**
      * Uses the AnnotationsPlugin interface to instantiate and return a list of every annotation currently visible to the gatk
      */
+    @SuppressWarnings("deprecation")
     public static List<Annotation> getAllAnnotations() {
         CommandLineParser clp = new CommandLineArgumentParser(
                 new Object(),