From bca436578f3ed9dcc6c7fdda5b0c458728675e26 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 19 Jan 2010 15:55:23 +0000
Subject: [PATCH] Added the -maxQ argument to the list of arguments in the PG
 tag

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2627 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/recalibration/TableRecalibrationWalker.java     | 1 +
 1 file changed, 1 insertion(+)

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 85c23768f..807b7865f 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -240,6 +240,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
                 }
             }
             commandLineString += "pQ=" + PRESERVE_QSCORES_LESS_THAN + ", ";
+            commandLineString += "maxQ=" + MAX_QUALITY_SCORE + ", ";
             commandLineString += "smoothing=" + SMOOTHING;
             programRecord.setCommandLine( commandLineString );
             header.addProgramRecord( programRecord );