From 9a0761cd8f208b01c7d5d68e29f94ff008a2b180 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 31 Jul 2009 15:25:22 +0000
Subject: [PATCH] accidentally committed some debug code

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1356 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/genotype/glf/GLFWriter.java               | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
index 59118f8b0..769e4dc30 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
@@ -92,12 +92,7 @@ public class GLFWriter implements GenotypeWriter {
                                 int readDepth,
                                 LikelihoodObject lhValues) {
 
-        getRidOfMe++;
-        if (getRidOfMe == 500) {
-            this.close();
-        } else if (getRidOfMe < 500) {
-                System.err.println(contig.getSequenceName() + ":" + genomicLoc);
-        // check if we've jumped to a new contig
+       // check if we've jumped to a new contig
         checkSequence(contig.getSequenceName(), contig.getSequenceLength());
 
         SinglePointCall call = new SinglePointCall(refBase,
@@ -107,7 +102,6 @@ public class GLFWriter implements GenotypeWriter {
                 lhValues.toDoubleArray());
         lastPos = genomicLoc;
         call.write(this.outputBinaryCodec);
-        }
     }
 
     /**