From a1d5a384f46aa1b6f3ef413926e158a726b41939 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 5 Feb 2010 18:08:53 +0000
Subject: [PATCH] Reverting the last reversal. bestConsensus points to
 something also kept in a set, so just reassigning it will NOT automatically
 destroy the underlying data; explicit clearing of unneeded data reinstated.
 STUPIDO!!!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2796 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java | 1 +
 .../sting/gatk/walkers/indels/IntervalCleanerWalker.java         | 1 +
 2 files changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 9947ea054..d6f82245a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -460,6 +460,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
             //logger.debug(consensus.str +  " " + consensus.mismatchSum);
             if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
+                if ( bestConsensus != null ) bestConsensus.readIndexes.clear();
                 bestConsensus = consensus;
                 //logger.debug(consensus.str +  " " + consensus.mismatchSum);
             } else {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
index b7caee706..390a80c21 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
@@ -365,6 +365,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
 
             //logger.debug(consensus.str +  " " + consensus.mismatchSum);
             if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
+                if ( bestConsensus != null ) bestConsensus.readIndexes.clear();
                 bestConsensus = consensus;
                 //logger.debug(consensus.str +  " " + consensus.mismatchSum);
             } else {