Prevent close from hiding causal exceptions #528

* Exceptions thrown by a tool can be hidden by unsafe close methods throwing additional exceptions.
  Avoid this by making use of try-with-resources suppressed exception handling in order to surface the
  primary exception as well as the secondary ones.

* Fixes #528

src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgram.java

@@ -132,15 +132,19 @@ protected void onShutdown() {}
     /**
      * Template method that runs the startup hook, doWork and then the shutdown hook.
      */
+    @SuppressWarnings("try")
     public final Object runTool(){
-        try {
+        try(
+            final AutoCloseableNoCheckedExceptions thisTool =
+                    () -> {
+                        logger.info("Shutting down engine");
+                        onShutdown();
+                    }
+            ) {
             logger.info("Initializing engine");
             onStartup();
             logger.info("Done initializing engine");
             return doWork();
-        } finally {
-            logger.info("Shutting down engine");
-            onShutdown();
         }
     }
 
@@ -483,4 +487,8 @@ public final CommandLineParser getCommandLineParser() {
         }
         return commandLineParser;
     }
+
+    protected interface AutoCloseableNoCheckedExceptions extends AutoCloseable{
+        @Override void close();
+    }
 }

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

@@ -1078,17 +1078,17 @@ public void onTraversalStart() {}
     public Object onTraversalSuccess() { return null; }
 
     @Override
+    @SuppressWarnings("try")
     protected final Object doWork() {
-        try {
+        //todo update when we move to java 9+
+        try(final AutoCloseableNoCheckedExceptions thisTool = this::closeTool){
             onTraversalStart();
             progressMeter.start();
             traverse();
             if (!progressMeter.stopped()) {
                 progressMeter.stop();
             }
             return onTraversalSuccess();
-        } finally {
-            closeTool();
         }
     }