From 870e65a6859c7d4c066aeb2d0fd18f3e1fb5c82e Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 3 May 2011 02:09:53 +0000
Subject: [PATCH] Fixing a build failure because I want to be completely sure
 that the code I checked in immediately following the build breaking code
 passes integration tests.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5727 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/recalibration/TableRecalibrationWalker.java    | 2 +-
 .../IndelCountCovariates/IndelCountCovariatesWalker.java        | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index 4bf3e2381..0eaa1245e 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -122,7 +122,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
     private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
     private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
-    protected static final String EOF_MARKER = "EOF";
+    public static final String EOF_MARKER = "EOF";
     private long numReadsWithMalformedColorSpace = 0;
 
     /////////////////////////////
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java
index 3e983bb3c..a6166be53 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java
@@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 //import org.broadinstitute.sting.gatk.walkers.recalibration.*;
 //import org.broadinstitute.sting.gatk.walkers.recalibration.CountCovariatesGatherer;
+import org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.PluginManager;