From 6787f86803d067436d442030b519112154153221 Mon Sep 17 00:00:00 2001
From: Chris Hartl <chartl@broadinstitute.org>
Date: Wed, 9 Jan 2013 13:23:24 -0500
Subject: [PATCH] Eliminate the import of DiploidGenotype, which switched
 public/private underneath me but for some reason didn't stop me from
 compiling...

---
 .../sting/gatk/walkers/variantutils/ConcordanceMetrics.java   | 1 -
 .../sting/gatk/walkers/variantutils/GenotypeConcordance.java  | 4 ----
 2 files changed, 5 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
index ac6752277..f71bc4a01 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
@@ -4,7 +4,6 @@ import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
 import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.variant.variantcontext.*;
 import org.broadinstitute.variant.vcf.VCFHeader;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
index ff69b9b11..de7b14ddb 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
@@ -1,20 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.variantcontext.*;
 import org.broadinstitute.variant.vcf.VCFHeader;
-import org.broadinstitute.variant.vcf.VCFUtils;
 
 import java.io.PrintStream;
 import java.util.*;