From 9666d47d17d5083ee9acabcb2c8f58f9cc5db25d Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 14 Jun 2010 18:07:12 +0000
Subject: [PATCH] ooops, debug print now removed

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3550 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java              | 3 +--
 1 file changed, 1 insertion(+), 2 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 337a8758f..dcb87b79a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -171,7 +171,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             intervals = locs.iterator();
         }
         currentInterval = intervals.hasNext() ? intervals.next() : null;
- System.out.println("Interval: "+currentInterval);
+
         // set up the output writer(s)
         if ( baseWriterFilename != null ) {
             writers = new HashMap<String, SAMFileWriter>();
@@ -362,7 +362,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
         do {
             currentInterval = intervals.hasNext() ? intervals.next() : null;
-    System.out.println("Interval: "+currentInterval);
         } while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) );
 
         // call back into map now that the state has been updated