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Enough people have found this useful, so... 

Moving Callset Concordance tool to core and adding integration test.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2003 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-09 20:59:18 +00:00
parent 3793519bd4
commit 2fa2ae43ec
7 changed files with 42 additions and 6 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/CallsetConcordanceWalker.java → java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.concordance;
package org.broadinstitute.sting.gatk.walkers.concordance;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/ConcordanceType.java → java/src/org/broadinstitute/sting/gatk/walkers/concordance/ConcordanceType.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.concordance;
package org.broadinstitute.sting.gatk.walkers.concordance;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeCall;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/IndelSubsets.java → java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.concordance;
package org.broadinstitute.sting.gatk.walkers.concordance;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/NWayVenn.java → java/src/org/broadinstitute/sting/gatk/walkers/concordance/NWayVenn.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.concordance;
package org.broadinstitute.sting.gatk.walkers.concordance;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeCall;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java → java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.concordance;
package org.broadinstitute.sting.gatk.walkers.concordance;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.StingException;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java → java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.concordance;
package org.broadinstitute.sting.gatk.walkers.concordance;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.genotype.Variation;

36
java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java 100755
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@ -0,0 +1,36 @@
package org.broadinstitute.sting.gatk.walkers.concordance;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
public class CallsetConcordanceIntegrationTest extends WalkerTest {
public static String baseTestString() {
return "-T CallsetConcordance -R /broad/1KG/reference/human_b36_both.fasta -L 1:1-8000 -CO %s";
}
@Test
public void testSimpleVenn() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SimpleVenn", 1,
Arrays.asList("0a71c8f06b4179ba59cefad962cd034c"));
executeTest("testSimpleVenn", spec);
}
@Test
public void testSNPConcordance() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1,
Arrays.asList("5da8bf664813f0ab8b22070097f6900e"));
executeTest("testSNPConcordance", spec);
}
@Test
public void testNWayVenn() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -B set3,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/CEU.sample.vcf -CT NWayVenn", 1,
Arrays.asList("9da88442eea094da8b6110d8f5ed4408"));
executeTest("testNWayVenn", spec);
}
}