From cb95e68fc0aa64af4d63f50172e636357ac17ca4 Mon Sep 17 00:00:00 2001 From: kiran Date: Fri, 18 Feb 2011 07:17:35 +0000 Subject: [PATCH] CpG is no longer a standard stratification. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5273 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/varianteval/stratifications/CpG.java | 2 +- .../varianteval/VariantEvalIntegrationTest.java | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java index 9af9fd518..d940312b1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java @@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatc import java.util.ArrayList; import java.util.Set; -public class CpG extends VariantStratifier implements StandardStratification { +public class CpG extends VariantStratifier { private ArrayList states; @Override diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 7fe60e47a..4da7f995d 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -333,7 +333,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { public void testSelect1() { String extraArgs = "-L 1:1-10,000,000"; for (String tests : testsEnumerations) { - WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s", + WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s", 1, Arrays.asList("0eed0ea48cb55164ba8d9383b96811c9")); executeTestParallel("testSelect1", spec); //executeTest("testSelect1", spec); @@ -353,7 +353,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { public void testVEGenotypeConcordance() { String vcfFiles[] = {"GenotypeConcordanceEval.vcf", "GenotypeConcordanceEval.vcf.gz"}; for (String vcfFile : vcfFiles) { - WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", + WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", 1, Arrays.asList("1387fcf8d5c53ff2c820fe79cc999bcf")); executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); @@ -365,8 +365,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testVESimple() { HashMap expectations = new HashMap(); - expectations.put("-L 1:1-10,000,000", "60bbf3539212ff4ecb172e0ef848b297"); - expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "c4a178c58464e367a5a0b22a99f35b25"); + expectations.put("-L 1:1-10,000,000 -ST CpG", "60bbf3539212ff4ecb172e0ef848b297"); + expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "c4a178c58464e367a5a0b22a99f35b25"); for ( Map.Entry entry : expectations.entrySet() ) { String extraArgs = entry.getKey(); @@ -384,7 +384,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testVEComplex() { HashMap expectations = new HashMap(); - String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator" + + String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator -ST CpG" + " -B:dbsnp_130,dbSNP " + GATKDataLocation + "dbsnp_130_b36.rod" + " -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf"; @@ -408,7 +408,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testCompVsEvalAC() { - String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf"; + String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2b969088abbfe69337fc3af663278323")); executeTestParallel("testCompVsEvalAC",spec); //executeTest("testCompVsEvalAC",spec); @@ -420,7 +420,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testTranches() { - String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -tf " + testDir + "tranches.6.txt"; + String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("b018ca01b374def71fcd1bf164326485")); executeTestParallel("testTranches",spec); //executeTest("testTranches",spec);