From 27ddebee53e7d6b808c82dec5dd8849cd5014dd0 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 31 Aug 2012 13:41:03 -0400
Subject: [PATCH] Protect PrintReads from strange state from
 TraverseReadsUnitTests

---
 .../broadinstitute/sting/gatk/walkers/PrintReads.java | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
index dca23ae66..a5d4b45b6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
@@ -41,10 +41,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.File;
-import java.util.Collection;
-import java.util.Random;
-import java.util.Set;
-import java.util.TreeSet;
+import java.util.*;
 
 /**
  * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear in the input file.
@@ -141,6 +138,7 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
     public boolean simplifyReads = false;
     
 
+    List<ReadTransformer> readTransformers = Collections.emptyList();
     private TreeSet<String> samplesToChoose = new TreeSet<String>();
     private boolean SAMPLES_SPECIFIED = false;
     
@@ -153,6 +151,9 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
         if  ( platform != null )
             platform = platform.toUpperCase();
 
+        if ( getToolkit() != null )
+            readTransformers = getToolkit().getReadTransformers();
+
         Collection<String> samplesFromFile;
         if (!sampleFile.isEmpty())  {
             samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFile);
@@ -226,7 +227,7 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
     public GATKSAMRecord map( ReferenceContext ref, GATKSAMRecord readIn, RefMetaDataTracker metaDataTracker ) {
         GATKSAMRecord workingRead = readIn;
 
-        for ( final ReadTransformer transformer : getToolkit().getReadTransformers() ) {
+        for ( final ReadTransformer transformer : readTransformers ) {
             if ( logger.isDebugEnabled() ) logger.debug("Applying transformer " + transformer + " to read " + readIn.getReadName());
             workingRead = transformer.apply(workingRead);
         }