From 3d50c72d743d1f3838a7bf23fa9b5501a9282c97 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 19 Oct 2009 16:13:48 +0000
Subject: [PATCH] Forgot a dumb little System.out.println. You will be flooded
 with "This read will not be used." statements until, overwhelmed, you give in
 to my demands.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1874 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/BaseTransitionTableCalculatorJavaWalker.java    | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
index 352f6fa05..db3dc5abf 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
@@ -87,9 +87,9 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
                     // System.out.println("Base quality is: "+reads.get(r).getBaseQualities()[offsets.get(r)]);
                     // System.out.println("Read base is: "+ (char) reads.get(r).getReadBases()[offsets.get(r)]);
                     // System.out.println("Pileup is: " + map.getPileup().getBases());
-                    if ( ! useRead(reads.get(r),offsets.get(r),ref) ) {
-                        System.out.println("Read will not be used.");
-                    }
+                    // if ( ! useRead(reads.get(r),offsets.get(r),ref) ) {
+                    //    System.out.println("Read will not be used.");
+                    //}
                 }
                 if ( useRead( reads.get(r), offsets.get(r), ref ) ) {
                     updateTables( reads.get(r), offsets.get(r), map );