From cf7e6d0c0b69c8092e2c815831b56a3ce9552c94 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 5 Feb 2010 18:05:04 +0000
Subject: [PATCH] Memory-saving change, same as in old IntervalCleaner (if alt
 consensus does not beat the best one, destroy its data immediately)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2795 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java               | 2 ++
 1 file 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 c465882f2..9947ea054 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -462,6 +462,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
                 bestConsensus = consensus;
                 //logger.debug(consensus.str +  " " + consensus.mismatchSum);
+            } else {
+                consensus.readIndexes.clear(); // we do not need this alt consensus, release memory right away!!
             }
         }