From 04e5b28f6deeb88ab4a012535f574477e8b577de Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 19 Aug 2010 19:34:44 +0000
Subject: [PATCH] updates for VCF; we can no longer cache genotypes or alleles
 in a static array, this is bad for sharred memory parallel runs.  One
 instance per codec was better for performance than using ThreadLocal code.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4063 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
index 136529a52..e73f0bd78 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
@@ -57,11 +57,13 @@ public class CountRodWalker extends RodWalker<CountRodWalker.Datum, Pair<Expandi
         ExpandingArrayList<Long> nt = new ExpandingArrayList<Long>();
         nt.addAll(lhs.first);
         int index = 0;
-        for (Long l : rhs.first)
+        for (Long l : rhs.first) {
             if (nt.get(index) == null)
                 nt.add(l);
             else
                 nt.set(index,nt.get(index) + l);
+            index++;
+        }
         return new Pair<ExpandingArrayList<Long>, Long>(nt, lhs.second + rhs.second);
     }