From d61cafd19fa9415f16d5e57fa692925ce94ee242 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 19 Jan 2010 15:31:37 +0000
Subject: [PATCH] Make the formatting of the list of args in the PG tag
 consistent.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2626 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/recalibration/TableRecalibrationWalker.java   | 8 ++++----
 1 file changed, 4 insertions(+), 4 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 54cd3b3d6..85c23768f 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -222,12 +222,12 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         if( !NO_PG_TAG ) {
             final SAMProgramRecord programRecord = new SAMProgramRecord( "GATK TableRecalibration" );
             programRecord.setProgramVersion( RecalDataManager.versionString );
-            String commandLineString = "Covariates used = [";
+            String commandLineString = "Covariates=[";
             for( Covariate cov : requestedCovariates ) {
                 commandLineString += cov.getClass().getSimpleName() + ", ";
             }
             commandLineString = commandLineString.substring( 0, commandLineString.length() - 2 ); // Trim off the trailing comma
-            commandLineString += "] ";
+            commandLineString += "], ";
             // Add all of the arguments from the recalibration argument collection to the command line string
             final Field[] fields = RAC.getClass().getFields();
             for( Field field : fields ) {
@@ -239,8 +239,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
                     }
                 }
             }
-            commandLineString += "pQ = " + PRESERVE_QSCORES_LESS_THAN + ", ";
-            commandLineString += "smoothing = " + SMOOTHING;
+            commandLineString += "pQ=" + PRESERVE_QSCORES_LESS_THAN + ", ";
+            commandLineString += "smoothing=" + SMOOTHING;
             programRecord.setCommandLine( commandLineString );
             header.addProgramRecord( programRecord );