From 3289826892c6295a3cdd9056d8f0e1a27fa67124 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 25 Feb 2010 21:02:18 +0000
Subject: [PATCH] Fix chartl's issue -- reduceInit() is sometimes called
 unnecessarily at the end of a traversal.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2889 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/executive/Accumulator.java     | 20 ++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
index 8022cbcce..d24242613 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
@@ -123,6 +123,12 @@ public abstract class Accumulator {
      * and aggregates those results into a single list.
      */
     private static class IntervalAccumulator extends Accumulator {
+        /**
+         * True if a new interval is being started.  This flag is used to
+         * ensure that reduceInit() is not called unnecessarily.
+         */
+        private boolean startingNewInterval = true;
+
         /**
          * An iterator through all intervals in the series.
          */
@@ -138,19 +144,27 @@ public abstract class Accumulator {
          */
         private final List<Pair<GenomeLoc,Object>> intervalAccumulator = new ArrayList<Pair<GenomeLoc,Object>>();
 
+        /**
+         * Holds the next value to be passed in as the reduce result.
+         */
         private Object nextReduceInit = null;
 
         protected IntervalAccumulator(Walker walker, GenomeLocSortedSet intervals) {
             super(walker);
             this.intervalIterator = intervals.iterator();
             if(intervalIterator.hasNext()) currentInterval = intervalIterator.next();
-            nextReduceInit = walker.reduceInit();
         }
 
         /**
          * Interval accumulator always feeds reduceInit into every new traversal.
          */
-        public Object getReduceInit() { return nextReduceInit; }
+        public Object getReduceInit() {
+            if(startingNewInterval) {
+                startingNewInterval = false;
+                nextReduceInit = walker.reduceInit();
+            }
+            return nextReduceInit;
+        }
 
         /**
          * Create a holder for interval results if none exists.  Add the result to the holder.
@@ -164,7 +178,7 @@ public abstract class Accumulator {
 
             if(currentInterval != null && currentInterval.getContig().equals(location.getContig()) && currentInterval.getStop() == location.getStop()) {
                 intervalAccumulator.add(new Pair<GenomeLoc,Object>(currentInterval,result));
-                nextReduceInit = walker.reduceInit();
+                startingNewInterval = true;
             }
             else
                 nextReduceInit = result;