From bcda66d2db43365a0c7f21724e106067bbc84d0f Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 3 Jul 2009 16:45:23 +0000
Subject: [PATCH] Simple performance improvements

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1166 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/recalibration/CovariateCounterWalker.java  | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
index 8bf7ef47a..a2b41b6a2 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@@ -115,8 +115,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
     private boolean isSupportedReadGroup( SAMReadGroupRecord readGroup ) {
         for( String platform: platforms ) {
             platform = platform.trim();
-            if( readGroup.getAttribute("PL") == null ||
-                    platform.equals("*") ||
+            if( platform.equals("*") ||
+                    readGroup.getAttribute("PL") == null ||
                     readGroup.getAttribute("PL").toString().equalsIgnoreCase(platform) )
                 return true;
         }
@@ -208,7 +208,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
         for (String readGroup : new TreeSet<String>(covariateCounter.getReadGroups()) ) {
             for ( RecalData datum: RecalData.sort(covariateCounter.getRecalData(readGroup)) ) {
                 if ( datum.N > 0 )
-                    recalTableStream.format("%s%n", datum.toCSVString(collapsePos));
+                    recalTableStream.println(datum.toCSVString(collapsePos));
             }
         }
     }