From bc885b7bd017f89ea9ea1027b06b8bea20990c72 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 6 Dec 2010 20:57:11 +0000
Subject: [PATCH] Don't print debugging output.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4799 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java   | 2 +-
 java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
index d1e80a9ff..46f0a6972 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
@@ -243,7 +243,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     public void addAlignment( SAMRecord alignment ) {
         if ( engine.getArguments().BAQMode != BAQ.CalculationMode.NONE && engine.getWalkerBAQApplicationTime() == BAQ.ApplicationTime.ON_OUTPUT ) {
-            System.out.printf("Writing BAQ at OUTPUT TIME%n");
+            //System.out.printf("Writing BAQ at OUTPUT TIME%n");
             baqHMM.baqRead(alignment, engine.getReferenceDataSource().getReference(), engine.getArguments().BAQMode, engine.getWalkerBAQQualityMode());
         }
 
diff --git a/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java b/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
index b1db66e7e..c9e634e86 100644
--- a/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
+++ b/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
@@ -38,7 +38,7 @@ public class BAQSamIterator implements StingSAMIterator {
     }
 
     public SAMRecord next()     {
-        System.out.printf("BAQing during input%n");
+        //System.out.printf("BAQing during input%n");
         SAMRecord read = it.next();
         baqHMM.baqRead(read, refReader, cmode, qmode);
         return read;