From 615572ea06fb4b15be6964183cc30cbe886632ba Mon Sep 17 00:00:00 2001
From: kcibul <kcibul@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 17 Jun 2009 20:43:10 +0000
Subject: [PATCH] output to out... not System.out...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1034 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/SomaticMutationWalker.java | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
index c4e928b10..f0445d20c 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
@@ -314,7 +314,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
                             " QSUM was " + tumorReadPile.qualitySums.get(altAllele) +
                             " QSUM is now " + t2.qualitySums.get(altAllele);
 
-                    System.out.println(
+                    out.println(
                             context.getContig() + "\t" +
                                     context.getPosition() + "\t" +
                                     context.getPosition() + "\t"
@@ -333,7 +333,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
                 if (OUTPUT_FAILURES) {
                     String msg = "FAILED due to DISALIGNMENT TEST.";
 
-                    System.out.println(
+                    out.println(
                             context.getContig() + "\t" +
                                     context.getPosition() + "\t" +
                                     context.getPosition() + "\t"
@@ -368,7 +368,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
                         "__NAltSum: " + normalReadPile.qualitySums.get(altAllele) +
                         "__MIDP: " + midp.get(altAllele);
 
-            System.out.println(
+            out.println(
                     context.getContig() + "\t" +
                             context.getPosition() + "\t" +
                             context.getPosition() + "\t"
@@ -419,7 +419,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
                 char base = read.getReadString().charAt(offset);
 
                 // TODO: use a logger to output this information for debugging/Picard folks
-                //System.out.println("MMQSUM: Filtering out " + read.getReadName() + " with locus base " + base + " and ref of " + pile.refBase);
+                //out.println("MMQSUM: Filtering out " + read.getReadName() + " with locus base " + base + " and ref of " + pile.refBase);
             }
         }
         return newPile;
@@ -553,7 +553,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
             if ( mismatchScore > 0 ) {
 
                 if ( mismatchScore > 100) {
-                    System.out.println(read.getReadName() + " has a sum of mismatch quality scores of " + mismatchScore);
+                    out.println(read.getReadName() + " has a sum of mismatch quality scores of " + mismatchScore);
 
                 } else {
                     altReads.add(aRead);