From 99b942b0b41871c8e80bea6316868a1c80fd2ecc Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 1 Dec 2010 20:16:53 +0000
Subject: [PATCH] Removing duplicated header args

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4770 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/recalibration/TableRecalibrationWalker.java     | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index ebeb159f0..38cb18d20 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -271,12 +271,6 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
             }
             sb.setCharAt(sb.length()-2, ']');
             sb.setCharAt(sb.length()-1, ' ');
-            sb.append("pQ=");
-            sb.append(PRESERVE_QSCORES_LESS_THAN);
-            sb.append(" maxQ=");
-            sb.append(MAX_QUALITY_SCORE);
-            sb.append(" smoothing=");
-            sb.append(SMOOTHING);
             programRecord.setCommandLine(sb.toString());
 
             List<SAMProgramRecord> oldRecords = header.getProgramRecords();