Fix Java 11 deprecation warnings

src/main/java/org/broadinstitute/hellbender/Main.java

@@ -16,6 +16,7 @@
 
 import java.io.PrintStream;
 import java.io.Serializable;
+import java.lang.reflect.InvocationTargetException;
 import java.util.*;
 import java.util.jar.Attributes;
 import java.util.jar.Manifest;
@@ -346,12 +347,12 @@ private CommandLineProgram extractCommandLineProgram( final String[] args,
             if (simpleNameToClass.containsKey(args[0])) {
                 final Class<?> clazz = simpleNameToClass.get(args[0]);
                 try {
-                    final Object commandLineProgram = clazz.newInstance();
+                    final Object commandLineProgram = clazz.getDeclaredConstructor().newInstance();
                     // wrap Picard CommandLinePrograms in a PicardCommandLineProgramExecutor
                     return commandLineProgram instanceof picard.cmdline.CommandLineProgram ?
                             new PicardCommandLineProgramExecutor((picard.cmdline.CommandLineProgram) commandLineProgram) :
                             (CommandLineProgram) commandLineProgram;
-                } catch (final InstantiationException | IllegalAccessException e) {
+                } catch (final InstantiationException | IllegalAccessException | NoSuchMethodException | InvocationTargetException e) {
                     throw new RuntimeException(e);
                 }
             }
@@ -395,8 +396,8 @@ private void printUsage(final PrintStream destinationStream, final Set<Class<?>>
                 CommandLineProgramGroup programGroup = programGroupClassToProgramGroupInstance.get(property.programGroup());
                 if (null == programGroup) {
                     try {
-                        programGroup = property.programGroup().newInstance();
-                    } catch (final InstantiationException | IllegalAccessException e) {
+                        programGroup = property.programGroup().getDeclaredConstructor().newInstance();
+                    } catch (final InstantiationException | IllegalAccessException | NoSuchMethodException | InvocationTargetException e) {
                         throw new RuntimeException(e);
                     }
                     programGroupClassToProgramGroupInstance.put(property.programGroup(), programGroup);

src/main/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKAnnotationPluginDescriptor.java

@@ -187,6 +187,7 @@ public String getDisplayName()
      * @throws InstantiationException if thrown when calling the {@code pluginClass} constructor
      */
     @Override
+    @SuppressWarnings("deprecation")
     public Annotation createInstanceForPlugin(Class<?> pluggableClass) throws IllegalAccessException, InstantiationException {
         Annotation annot = null;
         final String simpleName = pluggableClass.getSimpleName();

src/main/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKReadFilterPluginDescriptor.java

@@ -137,6 +137,7 @@ public boolean includePluginClass(Class<?> c) {
 
     // Instantiate a new ReadFilter derived object and save it in the list
     @Override
+    @SuppressWarnings("deprecation")
     public ReadFilter createInstanceForPlugin(final Class<?> pluggableClass) throws IllegalAccessException, InstantiationException {
         ReadFilter readFilter = null;
         final String simpleName = pluggableClass.getSimpleName();

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

@@ -23,6 +23,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
 import java.nio.channels.SeekableByteChannel;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -347,8 +348,8 @@ private static <T extends Feature> FeatureReader<T> getFeatureReader(final Featu
             featureInput.setFeatureCodecClass((Class<FeatureCodec<T, ?>>) codec.getClass());
         } else {
             try {
-                codec = codecClass.newInstance();
-            } catch (final InstantiationException | IllegalAccessException e) {
+                codec = codecClass.getDeclaredConstructor().newInstance();
+            } catch (final InstantiationException | IllegalAccessException | NoSuchMethodException | InvocationTargetException e) {
                 throw new GATKException("Unable to automatically instantiate codec " + codecClass.getName());
             }
         }

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

@@ -22,6 +22,7 @@
 
 import java.io.File;
 import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.ParameterizedType;
 import java.lang.reflect.Type;
 import java.nio.file.Files;
@@ -519,12 +520,12 @@ private <T extends Feature> FeatureDataSource<T> lookupDataSource( final Feature
 
         for ( final Class<?> codecClass : DISCOVERED_CODECS ) {
             try {
-                final FeatureCodec<? extends Feature, ?> codec = (FeatureCodec<? extends Feature, ?>)codecClass.newInstance();
+                final FeatureCodec<? extends Feature, ?> codec = (FeatureCodec<? extends Feature, ?>)codecClass.getDeclaredConstructor().newInstance();
                 if ( codec.canDecode(featureFile.toAbsolutePath().toUri().toString()) ) {
                     candidateCodecs.add(codec);
                 }
             }
-            catch ( InstantiationException | IllegalAccessException e ) {
+            catch (InstantiationException | IllegalAccessException | NoSuchMethodException | InvocationTargetException e ) {
                 throw new GATKException("Unable to automatically instantiate codec " + codecClass.getName());
             }
         }

src/main/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyperEngine.java

@@ -200,7 +200,7 @@ public VariantContext finalizeGenotype(final VariantContext variant, final Varia
 
         for (final Class c : allASAnnotations) {
             try {
-                final InfoFieldAnnotation annotation = (InfoFieldAnnotation) c.newInstance();
+                final InfoFieldAnnotation annotation = (InfoFieldAnnotation) c.getDeclaredConstructor().newInstance();
                 if (annotation instanceof AS_StandardAnnotation && annotation instanceof ReducibleAnnotation) {
                     final ReducibleAnnotation ann = (ReducibleAnnotation) annotation;
                     if (variant.hasAttribute(ann.getRawKeyName())) {
@@ -222,7 +222,7 @@ public VariantContext finalizeGenotype(final VariantContext variant, final Varia
         if (!keepAllSites) {
             for (final Class c : allASAnnotations) {
                 try {
-                    final InfoFieldAnnotation annotation = (InfoFieldAnnotation) c.newInstance();
+                    final InfoFieldAnnotation annotation = (InfoFieldAnnotation) c.getDeclaredConstructor().newInstance();
                     if (annotation instanceof AS_StandardAnnotation && annotation instanceof ReducibleAnnotation) {
                         final ReducibleAnnotation ann = (ReducibleAnnotation) annotation;
                         if (variant.hasAttribute(ann.getRawKeyName())) {

src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java

@@ -8,7 +8,9 @@
 import org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval;
 import org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager;
+import org.broadinstitute.hellbender.utils.ClassUtils;
 
+import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
@@ -30,15 +32,9 @@ private EvaluationContext(final VariantEval walker, final Set<Class<? extends Va
         this.evaluationInstances = new ArrayList<>(evaluationClasses.size());
 
         for ( final Class<? extends VariantEvaluator> c : evaluationClasses ) {
-            try {
-                final VariantEvaluator eval = c.newInstance();
-                if ( doInitialize ) eval.initialize(walker);
-                evaluationInstances.add(eval);
-            } catch (InstantiationException e) {
-                throw new GATKException("Unable to instantiate eval module '" + c.getSimpleName() + "'", e);
-            } catch (IllegalAccessException e) {
-                throw new GATKException("Illegal access error when trying to instantiate eval module '" + c.getSimpleName() + "'", e);
-            }
+            final VariantEvaluator eval = ClassUtils.makeInstanceOf(c);
+            if ( doInitialize ) eval.initialize(walker);
+            evaluationInstances.add(eval);
         }
     }
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/VariantEvalUtils.java

@@ -16,6 +16,7 @@
 import org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.RequiredStratification;
 import org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.StandardStratification;
 import org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier;
+import org.broadinstitute.hellbender.utils.ClassUtils;
 import org.broadinstitute.hellbender.utils.samples.Sample;
 import org.reflections.Reflections;
 
@@ -120,17 +121,10 @@ public List<VariantStratifier> initializeStratificationObjects(boolean noStandar
             if (stratifierClasses.containsKey(module)) {
                 Class<? extends VariantStratifier> c = stratifierClasses.get(module);
 
-                try {
-                    VariantStratifier vs = c.newInstance();
-                    vs.setVariantEvalWalker(variantEvalWalker);
-                    vs.initialize();
-
-                    strats.add(vs);
-                } catch (InstantiationException e) {
-                    throw new GATKException("Unable to instantiate stratification module '" + c.getSimpleName() + "'");
-                } catch (IllegalAccessException e) {
-                    throw new GATKException("Illegal access error when trying to instantiate stratification module '" + c.getSimpleName() + "'");
-                }
+                VariantStratifier vs = ClassUtils.makeInstanceOf(c);
+                vs.setVariantEvalWalker(variantEvalWalker);
+                vs.initialize();
+                strats.add(vs);
             }
         }
 

src/main/java/org/broadinstitute/hellbender/utils/ClassUtils.java

@@ -3,6 +3,7 @@
 import org.broadinstitute.barclay.argparser.ClassFinder;
 import org.broadinstitute.hellbender.exceptions.GATKException;
 
+import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Modifier;
 import java.util.ArrayList;
 import java.util.List;
@@ -68,8 +69,8 @@ public static <T> List<T> makeInstancesOfSubclasses(final Class<? extends T> cla
     public static <T> T makeInstanceOf(final Class<T> clazz) {
         if (canMakeInstances(clazz)) {
             try {
-                return clazz.newInstance();
-            } catch (final InstantiationException | IllegalAccessException e) {
+                return clazz.getDeclaredConstructor().newInstance();
+            } catch (final InstantiationException | IllegalAccessException | NoSuchMethodException | InvocationTargetException e) {
                 throw new GATKException("Problem making an instance of " + clazz + " Do check that the class has a non-arg constructor", e);
             }
         }

src/main/java/org/broadinstitute/hellbender/utils/help/GATKDocWorkUnit.java

@@ -1,6 +1,5 @@
 package org.broadinstitute.hellbender.utils.help;
 
-import com.sun.javadoc.ClassDoc;
 import org.broadinstitute.barclay.help.DocWorkUnit;
 import org.broadinstitute.barclay.help.DocWorkUnitHandler;
 import org.broadinstitute.barclay.help.DocumentedFeature;
@@ -15,12 +14,13 @@
  * by methods that are used by the GATK runtime. This class has a dependency on com.sun.javadoc classes,
  * which may not be present since they're not provided as part of the normal GATK runtime classpath.
  */
+@SuppressWarnings("removal")
 public class GATKDocWorkUnit extends DocWorkUnit {
 
     public GATKDocWorkUnit(
             final DocWorkUnitHandler workUnitHandler,
             final DocumentedFeature documentedFeatureAnnotation,
-            final ClassDoc classDoc,
+            final com.sun.javadoc.ClassDoc classDoc,
             final Class<?> clazz) {
         super(workUnitHandler, documentedFeatureAnnotation, classDoc, clazz);
     }

src/main/java/org/broadinstitute/hellbender/utils/help/GATKHelpDoclet.java

@@ -1,8 +1,5 @@
 package org.broadinstitute.hellbender.utils.help;
 
-import com.sun.javadoc.ClassDoc;
-import com.sun.javadoc.RootDoc;
-
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.barclay.help.DocWorkUnit;
 import org.broadinstitute.barclay.help.GSONWorkUnit;
@@ -19,6 +16,7 @@
  * by methods that are used by the GATK runtime. This class has a dependency on com.sun.javadoc classes,
  * which may not be present since they're not provided as part of the normal GATK runtime classpath.
  */
+@SuppressWarnings("removal")
 public class GATKHelpDoclet extends HelpDoclet {
 
     private final static String GATK_FREEMARKER_INDEX_TEMPLATE_NAME = "generic.index.template.html";
@@ -29,7 +27,7 @@ public class GATKHelpDoclet extends HelpDoclet {
      * @param rootDoc
      * @throws IOException
      */
-    public static boolean start(final RootDoc rootDoc) throws IOException {
+    public static boolean start(final com.sun.javadoc.RootDoc rootDoc) throws IOException {
         return new GATKHelpDoclet().startProcessDocs(rootDoc);
     }
 
@@ -55,7 +53,7 @@ public String getIndexTemplateName() {
     @Override
     protected DocWorkUnit createWorkUnit(
             final DocumentedFeature documentedFeature,
-            final ClassDoc classDoc,
+            final com.sun.javadoc.ClassDoc classDoc,
             final Class<?> clazz)
     {
         return new GATKDocWorkUnit(

src/main/java/org/broadinstitute/hellbender/utils/runtime/ProcessControllerBase.java

@@ -112,6 +112,7 @@ public Process getProcess() {
     abstract void tryCleanShutdown();
 
     @Override
+    @SuppressWarnings("deprecation")
     protected void finalize() throws Throwable {
         try {
             tryCleanShutdown();

src/test/java/org/broadinstitute/hellbender/engine/FeatureManagerUnitTest.java

@@ -49,7 +49,7 @@ public void testDetectCorrectFileFormat( final File file, final Class<? extends
 
         // We should also get the correct codec if we pass in the explicit expected Feature type to getCodecForFile()
         @SuppressWarnings("unchecked")
-        final Class<? extends Feature> expectedCodecFeatureType = expectedCodecClass.newInstance().getFeatureType();
+        final Class<? extends Feature> expectedCodecFeatureType = expectedCodecClass.getDeclaredConstructor().newInstance().getFeatureType();
         Assert.assertEquals(FeatureManager.getCodecForFile(file, expectedCodecFeatureType).getClass(), expectedCodecClass,
                 "Wrong codec selected for file " + file.getAbsolutePath() + " after subsetting to the expected Feature type");
     }

src/test/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtilsUnitTest.java

@@ -88,10 +88,10 @@ public void testNormalizeScientificNotation(Object toNormalize, Object expected)
     public Object[][] getIntegerValuesToNormalize(){
         final Object aSpecificObject = new Object();
         return new Object[][] {
-                {"27", new Integer(27)},
-                {"-27", new Integer(-27)},
-                {"0", new Integer(0)},
-                {"-27014", new Integer(-27014)},
+                {"27", 27},
+                {"-27", -27},
+                {"0", 0},
+                {"-27014", -27014},
                 {1, 1},
                 {1, 1},
                 {-1, -1},

src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java

@@ -1143,10 +1143,10 @@ public void testVcfMafConcordance(final String inputVcf,
                 mafFieldValues = maf.getRecords().stream().map(AnnotatedInterval::getContig).collect(Collectors.toList());
             }
             else if ( annotationsToCheckMaf.get(i).equals(MafOutputRendererConstants.FieldName_Start_Position) ) {
-                mafFieldValues = maf.getRecords().stream().map(AnnotatedInterval::getStart).map(x -> new Integer(x)).map(Object::toString).collect(Collectors.toList());
+                mafFieldValues = maf.getRecords().stream().map(AnnotatedInterval::getStart).map(Object::toString).collect(Collectors.toList());
             }
             else if ( annotationsToCheckMaf.get(i).equals(MafOutputRendererConstants.FieldName_End_Position) ) {
-                mafFieldValues = maf.getRecords().stream().map(AnnotatedInterval::getEnd).map(x -> new Integer(x)).map(Object::toString).collect(Collectors.toList());
+                mafFieldValues = maf.getRecords().stream().map(AnnotatedInterval::getEnd).map(Object::toString).collect(Collectors.toList());
             }
             else if ( annotationsToCheckMaf.get(i).equals(MafOutputRendererConstants.FieldName_Hugo_Symbol) ) {
                 mafFieldValues = maf.getRecords().stream().map(x -> x.getAnnotationValue(MafOutputRendererConstants.FieldName_Hugo_Symbol)).map(a -> a.isEmpty() ? "Unknown" : a).collect(Collectors.toList());

src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqScoreIntegrationTest.java

@@ -43,11 +43,11 @@ private static Map<String, PSPathogenTaxonScore> getScores(final String[] lines)
             final PSPathogenTaxonScore score = new PSPathogenTaxonScore();
             final String taxonId = tok[0];
             score.setKingdomTaxonId(Math.abs(tok[4].hashCode()));
-            score.addSelfScore(new Double(tok[5]));
-            score.addScoreNormalized(new Double(tok[6]));
-            score.addTotalReads(new Integer(tok[7]));
-            score.addUnambiguousReads(new Integer(tok[8]));
-            score.setReferenceLength(new Long(tok[9]));
+            score.addSelfScore(Double.parseDouble(tok[5]));
+            score.addScoreNormalized(Double.parseDouble(tok[6]));
+            score.addTotalReads(Integer.parseInt(tok[7]));
+            score.addUnambiguousReads(Integer.parseInt((tok[8])));
+            score.setReferenceLength(Long.parseLong(tok[9]));
             Assert.assertFalse(scores.containsKey(taxonId), "Found more than one entry for taxon ID " + taxonId);
             scores.put(taxonId, score);
         }

src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/SVKmerShortUnitTest.java

@@ -104,7 +104,7 @@ public void testRandomMaskedKmers() {
             //Generate random indices to mask
             List<Byte> maskIndices = new ArrayList<>(K);
             for (int j = 0; j < K; j++) {
-                maskIndices.add(new Byte((byte) j));
+                maskIndices.add((byte) j);
             }
             Collections.shuffle(maskIndices);
             int maskSize = rand.nextInt(K - 3) + 2;

src/test/java/org/broadinstitute/hellbender/tools/spark/utils/LargeLongHopscotchSetTest.java

@@ -132,7 +132,7 @@ void resizeTest() {
         Assert.assertTrue(hopscotchSet.size() == hashSet.size());
         LongIterator itrL = hopscotchSet.iterator();
         while (itrL.hasNext()) {
-            Assert.assertTrue(hashSet.contains(new Long(itrL.next())));
+            Assert.assertTrue(hashSet.contains(itrL.next()));
         }
         for (Long val : hashSet) {
             Assert.assertTrue(hopscotchSet.contains(val.longValue()));
@@ -155,7 +155,7 @@ void loadRandomLongsTest() {
         for (int valNo = 0; valNo != HHASH_NVALS; ++valNo) {
             final long randLong = randomLong(rng);
             hopscotchSet.add(randLong);
-            hashSet.add(new Long(randLong));
+            hashSet.add(randLong);
         }
         Assert.assertEquals(hashSet.size(), hopscotchSet.size());
         for (final Long val : hashSet) {

src/test/java/org/broadinstitute/hellbender/tools/spark/utils/LongBloomFilterTest.java

@@ -84,7 +84,7 @@ void testRandomLongs() {
         final LongBloomFilter bloomFilter = new LongBloomFilter(HHASH_NVALS, FPP);
         for (int valNo = 0; valNo != HHASH_NVALS; ++valNo) {
             final long randLong = randomLong(rng);
-            hashSet.add(new Long(randLong));
+            hashSet.add(randLong);
             bloomFilter.add(randLong);
         }
         for (final Long val : hashSet) {
@@ -94,7 +94,7 @@ void testRandomLongs() {
         int num_total = 0;
         for (int valNo = 0; valNo != FPR_NVALS; ++valNo) {
             final long randLong = randomLong(rng);
-            if (!hashSet.contains(new Long(randLong))) {
+            if (!hashSet.contains(randLong)) {
                 num_total++;
                 if (bloomFilter.contains(randLong)) {
                     num_false_pos++;