diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java similarity index 98% rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java index 139c16441..e0956f7bf 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/DbSNPPercentage.java similarity index 91% rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/DbSNPPercentage.java index 95daf705e..74a13ea24 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/DbSNPPercentage.java @@ -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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java similarity index 99% rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/GenotypeConcordance.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java index 113367f9c..a8b16df27 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java @@ -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.*; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java similarity index 99% rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java index 6015e0a64..6ee35ba78 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java similarity index 97% rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java index 1737b8471..b059b6bea 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/ValidationRate.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationRate.java similarity index 98% rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/ValidationRate.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationRate.java index bf44c7c9f..eba2741b0 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/ValidationRate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationRate.java @@ -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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2Walker.java similarity index 99% rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2Walker.java index 282023b4f..b2ec2ab0c 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2Walker.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvaluator.java similarity index 97% rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvaluator.java index 242512f49..7312dfcd7 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvaluator.java @@ -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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantQualityScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java similarity index 99% rename from java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantQualityScore.java rename to java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java index 7e8ede970..1054756bc 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantQualityScore.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.java index c3d8b79de..167ae98ad 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.java index 0acfb475c..3ef4f52eb 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java index 216323fbc..db40bf912 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java @@ -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; diff --git a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2IntegrationTest.java similarity index 97% rename from java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java rename to java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2IntegrationTest.java index 0438faaa7..ca9f9fb8c 100755 --- a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval2IntegrationTest.java @@ -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; diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableUnitTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableUnitTest.java deleted file mode 100755 index 001a0f450..000000000 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableUnitTest.java +++ /dev/null @@ -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> oneHom = new ArrayList>(4); - oneHom.add(new Pair(ref1,null)); - oneHom.add(new Pair(null,null)); - oneHom.add(new Pair(ref2,null)); - oneHom.add(new Pair(ref3,null)); - oneHom.add(new Pair(hom2,null)); - - List> oneHet = new ArrayList>(4); - oneHet.add(new Pair(ref1,null)); - oneHet.add(new Pair(ref2,null)); - oneHet.add(new Pair(ref3,null)); - oneHet.add(new Pair(null,null)); - oneHet.add(new Pair(het1,null)); - - List> twoHetOneHom = new ArrayList>(5); - twoHetOneHom.add(new Pair(ref1,null)); - twoHetOneHom.add(new Pair(ref2,null)); - twoHetOneHom.add(new Pair(ref3,null)); - twoHetOneHom.add(new Pair(het1,null)); - twoHetOneHom.add(new Pair(het2,null)); - twoHetOneHom.add(new Pair(hom1,null)); - - List> twoHetTwoHom = new ArrayList>(7); - twoHetTwoHom.add(new Pair(ref1,null)); - twoHetTwoHom.add(new Pair(ref2,null)); - twoHetTwoHom.add(new Pair(null,null)); - twoHetTwoHom.add(new Pair(ref3,null)); - twoHetTwoHom.add(new Pair(het1,null)); - twoHetTwoHom.add(new Pair(het2,null)); - twoHetTwoHom.add(new Pair(hom1,null)); - twoHetTwoHom.add(new Pair(hom2,null)); - - List> hetHomNoRef = new ArrayList>(2); - hetHomNoRef.add(new Pair(het2,null)); - hetHomNoRef.add(new Pair(hom2,null)); - - List> homNoRef = new ArrayList>(1); - homNoRef.add(new Pair(hom1,null)); - - Pair> countShouldBeOne = ctt.getPooledAlleleFrequency(oneHet,'G'); - Pair> countShouldBeTwo = ctt.getPooledAlleleFrequency(oneHom,'G'); - Pair> countShouldBeFour = ctt.getPooledAlleleFrequency(twoHetOneHom,'G'); - Pair> countShouldBeSix = ctt.getPooledAlleleFrequency(twoHetTwoHom,'G'); - Pair> countShouldBeThree = ctt.getPooledAlleleFrequency(hetHomNoRef,'G'); - Pair> 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); - } -}