From 4ed06801a72508d64e54cfa59f46ee546b5c74e0 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 2 Feb 2012 10:17:04 -0500
Subject: [PATCH] Updating HaplotypeCaller's HMM calc to use GOP as a function
 of the read instead of a function of the haplotype in preparation for IQSR

---
 .../gatk/walkers/recalibration/CountCovariatesWalker.java    | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
index bdf25419f..fdfb29da6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
@@ -357,11 +357,11 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
                 final GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
                 int offset = p.getOffset();
 
-                if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE  ) ) {
+                if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE ) ) {
                     continue;
                 }
 
-                if( !gatkRead.containsTemporaryAttribute( SEEN_ATTRIBUTE  ) )
+                if( !gatkRead.containsTemporaryAttribute( SEEN_ATTRIBUTE ) )
                 {
                     gatkRead.setTemporaryAttribute( SEEN_ATTRIBUTE, true );
                     RecalDataManager.parseSAMRecord( gatkRead, RAC );
@@ -377,7 +377,6 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
                             RecalDataManager.computeCovariates( gatkRead, requestedCovariates ));
                 }
 
-
                 // Skip this position if base quality is zero
                 if( gatkRead.getBaseQualities()[offset] > 0 ) {