From 30a104228aa1a5d44ad8d6e11c9c66b929beb3a6 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 22 Aug 2010 02:44:38 +0000
Subject: [PATCH] Don't require entropy reduction when cleaning only at known
 sites; instead we need to trust the known indels.  This will improve
 consistency between lane-level and aggregated cleaning.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4076 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java               | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 b3f5ef1c1..a317afced 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -533,7 +533,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 if ( !updateRead(bestConsensus.cigar, bestConsensus.positionOnReference, indexPair.second, aRead, (int)leftmostIndex) )
                     return;
             }
-            if ( !alternateReducesEntropy(altReads, reference, leftmostIndex) ) {
+            if ( !USE_KNOWN_INDELS_ONLY && !alternateReducesEntropy(altReads, reference, leftmostIndex) ) {
                 if ( statsOutput != null ) {
                     try {
                         statsOutput.write(currentInterval.toString());