From bb6c0db783e80cefc5719467c85d304a86fc13f7 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 7 Jun 2011 15:13:58 +0000
Subject: [PATCH] We found the cause of the inconsistency.  Woo hoo!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5955 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java         | 8 --------
 1 file changed, 8 deletions(-)

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 797af9ff3..484981e44 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -1567,14 +1567,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 loc = getToolkit().getGenomeLocParser().createGenomeLoc(loc.getContig(), padLeft, padRight);
                 reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
                 StringUtil.toUpperCase(reference);
-
-                // TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
-                if ( OUT_STATS != null ) {
-                    logger.warn("ERIC: padLeft = " + padLeft);
-                    logger.warn("ERIC: padRight = " + padRight);
-                    logger.warn("ERIC: loc = " + loc);
-                    logger.warn("ERIC: reference = " + new String(reference));
-                }
             }
 
             return reference;