From a2d90a35903d28ea4e7ab7017e712a008bc12712 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Wed, 20 Jul 2011 10:23:10 -0400
Subject: [PATCH] Bug fix: reverted logic so that default behavior skips over
 sample lookup

---
 .../sting/gatk/walkers/PrintReadsWalker.java              | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
index b10486e50..2b7db8d34 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
@@ -64,7 +64,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
     public Set<String> sampleNames = new TreeSet<String>();
 
     private TreeSet<String> samplesToChoose = new TreeSet<String>();
-    private boolean NO_SAMPLES_SPECIFIED = false;
+    private boolean SAMPLES_SPECIFIED = false;
 
     /**
      * The initialize function.
@@ -82,8 +82,8 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
         if (!sampleNames.isEmpty())
             samplesToChoose.addAll(sampleNames);
 
-        if(samplesToChoose.isEmpty()) {
-            NO_SAMPLES_SPECIFIED = true;
+        if(!samplesToChoose.isEmpty()) {
+            SAMPLES_SPECIFIED = true;
         }
 
     }
@@ -112,7 +112,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
             if ( readPlatformAttr == null || !readPlatformAttr.toString().toUpperCase().contains(platform))
                 return false;
         }
-        if (!NO_SAMPLES_SPECIFIED )  {
+        if (SAMPLES_SPECIFIED )  {
             // user specified samples to select
             String readSample = read.getReadGroup().getSample();
             boolean  found = false;