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Fixed discordance bug reported by Brad Chapman 

discordance now reports discordance between genotypes as well (just like concordance)
This commit is contained in:
Mauricio Carneiro 2012-01-30 09:50:14 -05:00
parent f1e07f169e
commit d5d4fa8a88
2 changed files with 10 additions and 12 deletions
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20
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -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;
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -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);