From 617eebd2045e95928f739d0d067d13ac6cc4db02 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 3 Jul 2012 14:55:37 -0400
Subject: [PATCH] More misc cleanup

---
 .../broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java | 1 -
 1 file changed, 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java
index 662eb0556..7d55c620b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java
@@ -82,7 +82,6 @@ public class ContextCovariate implements StandardCovariate {
     @Override
     public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
 
-        // TODO -- wrong: fix me
         final GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS);   // Write N's over the low quality tail of the reads to avoid adding them into the context
         
         final boolean negativeStrand = clippedRead.getReadNegativeStrandFlag();