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Moving VE2 to core; calling it "VariantEval" (one more checkin coming) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3179 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-15 20:25:47 +00:00
parent ac6f6363ce
commit e702bea99f
14 changed files with 20 additions and 136 deletions
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2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

16
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/DbSNPPercentage.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -21,25 +21,25 @@ import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
public class DbSNPPercentage extends VariantEvaluator {
@DataPoint(name = "DbSNP count", description = "number of DPSNP sites")
private long nDBSNPs = 0;
long nDBSNPs = 0;
@DataPoint(name = "total count", description = "number of total snp sites")
private long nEvalSNPs = 0;
long nEvalSNPs = 0;
@DataPoint(name = "novel snps", description = "number of total snp sites")
private long novelSites = 0;
long novelSites = 0;
@DataPoint(name = "snps at comp", description = "number of SNP sites at comp sites")
private long nSNPsAtComp = 0;
long nSNPsAtComp = 0;
@DataPoint(name = "% snps at comp", description = "percentage of SNP sites at comp sites")
private double compRate = 0.0;
double compRate = 0.0;
@DataPoint(name = "concordant", description = "number of concordant sites")
private long nConcordant = 0;
long nConcordant = 0;
@DataPoint(name = "% concordant", description = "the concordance rate")
private double concordantRate = 0.0;
double concordantRate = 0.0;
public DbSNPPercentage(VariantEval2Walker parent) {
// don't do anything

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/GenotypeConcordance.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.*;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

5
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/ValidationRate.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationRate.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -7,9 +7,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import java.util.List;
import java.util.Arrays;
/**
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2Walker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvaluator.java
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@ -1,12 +1,10 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import java.util.List;
/**
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantQualityScore.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.java
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@ -10,7 +10,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.oneoffprojects.walkers.varianteval2.MendelianViolationEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.java
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@ -12,7 +12,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.oneoffprojects.walkers.varianteval2.MendelianViolationEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator;
import java.util.EnumSet;
import java.util.Arrays;

9
java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
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@ -1,22 +1,17 @@
package org.broadinstitute.sting.playground.gatk.walkers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
import org.broadinstitute.sting.gatk.contexts.variantcontext.MutableVariantContext;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariationRod;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper;
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
import org.broadinstitute.sting.utils.StingException;
@ -24,9 +19,7 @@ import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
import org.broadinstitute.sting.oneoffprojects.walkers.varianteval2.MendelianViolationEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator;
import java.util.*;
import java.io.File;

2
java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java → java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2IntegrationTest.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;

104
java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableUnitTest.java
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@ -1,104 +0,0 @@
package org.broadinstitute.sting.playground.gatk.walkers;
import org.junit.Test;
import org.junit.Assert;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.BasicGenotype;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.gatk.walkers.varianteval.ConcordanceTruthTable;
import org.broadinstitute.sting.BaseTest;
import java.util.List;
import java.util.ArrayList;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Nov 19, 2009
* Time: 9:40:51 AM
* To change this template use File | Settings | File Templates.
*/
public class ConcordanceTruthTableUnitTest extends BaseTest {
@Test
public void testAlleleFrequencyCalculation() {
ConcordanceTruthTable ctt = new ConcordanceTruthTable(3);
// this will test the count of non-reference alleles at a T/G polymorphic site
Genotype ref1 = new BasicGenotype(null,"GG","G",30);
Genotype ref2 = new BasicGenotype(null,"GG","G",30);
Genotype ref3 = new BasicGenotype(null,"GG","G",30);
Genotype het1 = new BasicGenotype(null,"GT","G",32);
Genotype het2 = new BasicGenotype(null,"GT","G",28);
Genotype hom1 = new BasicGenotype(null,"TT","G",40);
Genotype hom2 = new BasicGenotype(null,"TT","G",27);
List<Pair<Genotype,Genotype>> oneHom = new ArrayList<Pair<Genotype,Genotype>>(4);
oneHom.add(new Pair<Genotype,Genotype>(ref1,null));
oneHom.add(new Pair<Genotype,Genotype>(null,null));
oneHom.add(new Pair<Genotype,Genotype>(ref2,null));
oneHom.add(new Pair<Genotype,Genotype>(ref3,null));
oneHom.add(new Pair<Genotype,Genotype>(hom2,null));
List<Pair<Genotype,Genotype>> oneHet = new ArrayList<Pair<Genotype,Genotype>>(4);
oneHet.add(new Pair<Genotype,Genotype>(ref1,null));
oneHet.add(new Pair<Genotype,Genotype>(ref2,null));
oneHet.add(new Pair<Genotype,Genotype>(ref3,null));
oneHet.add(new Pair<Genotype,Genotype>(null,null));
oneHet.add(new Pair<Genotype,Genotype>(het1,null));
List<Pair<Genotype,Genotype>> twoHetOneHom = new ArrayList<Pair<Genotype,Genotype>>(5);
twoHetOneHom.add(new Pair<Genotype,Genotype>(ref1,null));
twoHetOneHom.add(new Pair<Genotype,Genotype>(ref2,null));
twoHetOneHom.add(new Pair<Genotype,Genotype>(ref3,null));
twoHetOneHom.add(new Pair<Genotype,Genotype>(het1,null));
twoHetOneHom.add(new Pair<Genotype,Genotype>(het2,null));
twoHetOneHom.add(new Pair<Genotype,Genotype>(hom1,null));
List<Pair<Genotype,Genotype>> twoHetTwoHom = new ArrayList<Pair<Genotype,Genotype>>(7);
twoHetTwoHom.add(new Pair<Genotype,Genotype>(ref1,null));
twoHetTwoHom.add(new Pair<Genotype,Genotype>(ref2,null));
twoHetTwoHom.add(new Pair<Genotype,Genotype>(null,null));
twoHetTwoHom.add(new Pair<Genotype,Genotype>(ref3,null));
twoHetTwoHom.add(new Pair<Genotype,Genotype>(het1,null));
twoHetTwoHom.add(new Pair<Genotype,Genotype>(het2,null));
twoHetTwoHom.add(new Pair<Genotype,Genotype>(hom1,null));
twoHetTwoHom.add(new Pair<Genotype,Genotype>(hom2,null));
List<Pair<Genotype,Genotype>> hetHomNoRef = new ArrayList<Pair<Genotype,Genotype>>(2);
hetHomNoRef.add(new Pair<Genotype,Genotype>(het2,null));
hetHomNoRef.add(new Pair<Genotype,Genotype>(hom2,null));
List<Pair<Genotype,Genotype>> homNoRef = new ArrayList<Pair<Genotype,Genotype>>(1);
homNoRef.add(new Pair<Genotype,Genotype>(hom1,null));
Pair<Integer,Pair<Integer,Integer>> countShouldBeOne = ctt.getPooledAlleleFrequency(oneHet,'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeTwo = ctt.getPooledAlleleFrequency(oneHom,'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeFour = ctt.getPooledAlleleFrequency(twoHetOneHom,'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeSix = ctt.getPooledAlleleFrequency(twoHetTwoHom,'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeThree = ctt.getPooledAlleleFrequency(hetHomNoRef,'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeTwoHereToo = ctt.getPooledAlleleFrequency(homNoRef, 'G');
int expecChips = 4+4+6+7+2+1;
int numChips = countShouldBeOne.getSecond().getSecond() + countShouldBeTwo.getSecond().getSecond() +
countShouldBeFour.getSecond().getSecond() + countShouldBeSix.getSecond().getSecond() +
countShouldBeThree.getSecond().getSecond() + countShouldBeTwoHereToo.getSecond().getSecond();
logger.warn("Testing single het");
Assert.assertTrue(countShouldBeOne.getSecond().getFirst() == 1);
logger.warn("Testing single hom");
Assert.assertTrue(countShouldBeTwo.getSecond().getFirst() == 2);
logger.warn("Testing two hets + hom");
Assert.assertTrue(countShouldBeFour.getSecond().getFirst() == 4);
logger.warn("Testing two hets + two homs");
Assert.assertTrue(countShouldBeSix.getSecond().getFirst() == 6);
logger.warn("Testing het + hom without ref");
Assert.assertTrue(countShouldBeThree.getSecond().getFirst() == 3);
logger.warn("Testing hom without ref");
Assert.assertTrue(countShouldBeTwoHereToo.getSecond().getFirst() == 2);
logger.warn("Testing chip count sum");
Assert.assertTrue( expecChips == numChips);
}
}