From d5d4fa8a88ee599ea716ccdcecc0e6892b93e6eb Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 30 Jan 2012 09:50:14 -0500
Subject: [PATCH] Fixed discordance bug reported by Brad Chapman

discordance now reports discordance between genotypes as well (just like concordance)
---
 .../walkers/variantutils/SelectVariants.java  | 20 +++++++++----------
 .../SelectVariantsIntegrationTest.java        |  2 +-
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 6d94ffe6d..5eef7fb66 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -25,22 +25,20 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.sting.gatk.samples.Sample;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.MendelianViolation;
-import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+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.samples.Sample;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -557,7 +555,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
                 // Look for this sample in the all vcs of the comp ROD track.
                 boolean foundVariant = false;
                 for (VariantContext compVC : compVCs) {
-                    if (sampleHasVariant(compVC.getGenotype(g.getSampleName()))) {
+                    if (haveSameGenotypes(g, compVC.getGenotype(g.getSampleName()))) {
                         foundVariant = true;
                         break;
                     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index 042de2a27..9577966b7 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -58,7 +58,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s -NO_HEADER",
                 1,
-                Arrays.asList("78e6842325f1f1bc9ab30d5e7737ee6e")
+                Arrays.asList("929bbb96381541c162dc7e5462e26ea2")
         );
 
         executeTest("testDiscordance--" + testFile, spec);