Reverting old commits that made error handling better because ultimately they made things worse.

public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java

@@ -11,13 +11,17 @@ import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
 import java.util.Collection;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.Queue;
-import java.util.concurrent.*;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.FutureTask;
 
 /**
  * A microscheduler that schedules shards according to a tree-like structure.
@@ -40,6 +44,11 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
 
     private final Queue<TreeReduceTask> reduceTasks = new LinkedList<TreeReduceTask>();
 
+    /**
+     * An exception that's occurred in this traversal.  If null, no exception has occurred.
+     */
+    private RuntimeException error = null;
+
     /**
      * Queue of incoming shards.
      */
@@ -90,13 +99,11 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         ReduceTree reduceTree = new ReduceTree(this);
         initializeWalker(walker);
 
-        //
-        // exception handling here is a bit complex.  We used to catch and rethrow exceptions all over
-        // the place, but that just didn't work well.  Now we have a specific execution exception (inner class)
-        // to use for multi-threading specific exceptions.  All RuntimeExceptions that occur within the threads are rethrown
-        // up the stack as their underlying causes
-        //
         while (isShardTraversePending() || isTreeReducePending()) {
+            // Check for errors during execution.
+            if(hasTraversalErrorOccurred())
+                throw getTraversalError();
+
             // Too many files sitting around taking up space?  Merge them.
             if (isMergeLimitExceeded())
                 mergeExistingOutput(false);
@@ -123,8 +130,12 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
             result = reduceTree.getResult().get();
             notifyTraversalDone(walker,result);
         }
-        catch( InterruptedException ex ) { handleException(ex); }
+        catch (ReviewedStingException ex) {
-        catch( ExecutionException ex ) { handleException(ex); }
+            throw ex;
+        }
+        catch (Exception ex) {
+            throw new ReviewedStingException("Unable to retrieve result", ex);
+        }
 
         // do final cleanup operations
         outputTracker.close();
@@ -255,8 +266,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
                     // Specifically catch Tribble I/O exceptions and rethrow them as Reviewed.  We don't expect
                     // any issues here because we created the Tribble output file mere moments ago and expect it to
                     // be completely valid.
-                    final String reason = ex.getMessage();
+                    throw new ReviewedStingException("Unable to merge temporary Tribble output file.",ex);
-                    throw new ReviewedStingException("Unable to merge temporary Tribble output file" + (reason == null ? "." : (" (" + reason + ").")), ex);
                 }
             }
         }
@@ -328,39 +338,30 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
     }
 
     /**
-     * Handle an exception that occurred in a worker thread as needed by this scheduler.
+     * Detects whether an execution error has occurred.
-     *
+     * @return True if an error has occurred.  False otherwise.
-     * The way to use this function in a worker is:
-     *
-     * try { doSomeWork();
-     * catch ( InterruptedException ex ) { hms.handleException(ex); }
-     * catch ( ExecutionException ex ) { hms.handleException(ex); }
-     *
-     * @param ex the exception that occurred in the worker thread
      */
-    protected final void handleException(InterruptedException ex) {
+    private synchronized boolean hasTraversalErrorOccurred() {
-        throw new HierarchicalMicroScheduler.ExecutionFailure("Hierarchical reduce interrupted", ex);
+        return error != null;
+    }
+
+    private synchronized RuntimeException getTraversalError() {
+        if(!hasTraversalErrorOccurred())
+            throw new ReviewedStingException("User has attempted to retrieve a traversal error when none exists");
+        return error;
     }
 
     /**
-     * Handle an exception that occurred in a worker thread as needed by this scheduler.
+     * Allows other threads to notify of an error during traversal.
-     *
-     * The way to use this function in a worker is:
-     *
-     * try { doSomeWork();
-     * catch ( InterruptedException ex ) { hms.handleException(ex); }
-     * catch ( ExecutionException ex ) { hms.handleException(ex); }
-     *
-     * @param ex the exception that occurred in the worker thread
      */
-    protected final void handleException(ExecutionException ex) {
+    protected synchronized void notifyOfTraversalError(Throwable error) {
-        if ( ex.getCause() instanceof RuntimeException )
+        // If the error is already a Runtime, pass it along as is.  Otherwise, wrap it.
-            // if the cause was a runtime exception that's what we want to send up the stack
+        if (error instanceof RuntimeException)
-            throw (RuntimeException )ex.getCause();
+            this.error = (RuntimeException)error;
         else
-            throw new HierarchicalMicroScheduler.ExecutionFailure("Hierarchical reduce failed", ex);
+            this.error = new ReviewedStingException("An error occurred during the traversal.", error);
-    }
 
+    }
 
 
     /** A small wrapper class that provides the TreeReducer interface along with the FutureTask semantics. */
@@ -381,17 +382,6 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         }
     }
 
-    /**
-     * A specific exception class for HMS-specific failures such as
-     * Interrupted or ExecutionFailures that aren't clearly the fault
-     * of the underlying walker code
-     */
-    public static class ExecutionFailure extends ReviewedStingException {
-        public ExecutionFailure(final String s, final Throwable throwable) {
-            super(s, throwable);
-        }
-    }
-
     /**
      * Used by the ShardTraverser to report time consumed traversing a given shard.
      *

public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java

@@ -80,8 +80,8 @@ public class ShardTraverser implements Callable {
 
             return accumulator;
         } catch(Throwable t) {
-            // Notify that an exception has occurred
+            // Notify that an exception has occurred and rethrow it.
-            microScheduler.handleException(new ExecutionException(t));
+            microScheduler.notifyOfTraversalError(t);
             throw new RuntimeException(t);
         } finally {
             synchronized(this) {

public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java

@@ -79,8 +79,14 @@ public class TreeReducer implements Callable {
             else
                 result = walker.treeReduce( lhs.get(), rhs.get() );
         }
-        catch( InterruptedException ex ) { microScheduler.handleException(ex); }
+        catch( InterruptedException ex ) {
-        catch( ExecutionException ex ) { microScheduler.handleException(ex); }
+            microScheduler.notifyOfTraversalError(ex);
+            throw new ReviewedStingException("Hierarchical reduce interrupted", ex);
+        }
+        catch( ExecutionException ex ) {
+            microScheduler.notifyOfTraversalError(ex);
+            throw new ReviewedStingException("Hierarchical reduce failed", ex);
+        }
 
         final long endTime = System.currentTimeMillis();
 

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java

@@ -58,13 +58,11 @@ import java.util.ArrayList;
  * of poor base quality. This walker generates tables based on various user-specified covariates (such as read group,
  * reported quality score, cycle, and dinucleotide). Since there is a large amount of data one can then calculate an empirical
  * probability of error given the particular covariates seen at this site, where p(error) = num mismatches / num observations.
- * The output file is a CSV list of (the several covariate values, num observations, num mismatches, empirical quality score).
+ * The output file is a table (of the several covariate values, num observations, num mismatches, empirical quality score).
  * <p>
  * Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and will be added for the user regardless of whether or not they were specified.
  *
  * <p>
- * See the GATK wiki for a tutorial and example recalibration accuracy plots.
- * http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration
  *
  * <h2>Input</h2>
  * <p>