From 1861ca90fc0fd49ac04a369437b3e661089b0b49 Mon Sep 17 00:00:00 2001 From: kiran Date: Fri, 4 Mar 2011 15:36:07 +0000 Subject: [PATCH] A change to the definition of CpG sites (is now, from 5' to 3' a CG dinucleotide in the reference, and the CpG site is at the C, rather than either at the C or a G). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5373 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/varianteval/stratifications/CpG.java | 3 ++- .../varianteval/VariantEvalIntegrationTest.java | 16 ++++++++-------- 2 files changed, 10 insertions(+), 9 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 d940312b1..e9cb77dbb 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 @@ -32,7 +32,8 @@ public class CpG extends VariantStratifier { String leftFlank = fwRefBases.substring((fwRefBases.length()/2) - 1, (fwRefBases.length()/2) + 1); String rightFlank = fwRefBases.substring((fwRefBases.length()/2), (fwRefBases.length()/2) + 2); - if (leftFlank.equalsIgnoreCase("CG") || leftFlank.equalsIgnoreCase("GC") || rightFlank.equalsIgnoreCase("CG") || rightFlank.equalsIgnoreCase("GC")) { + //if (leftFlank.equalsIgnoreCase("CG") || leftFlank.equalsIgnoreCase("GC") || rightFlank.equalsIgnoreCase("CG") || rightFlank.equalsIgnoreCase("GC")) { + if (rightFlank.equalsIgnoreCase("CG")) { isCpG = true; } } 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 c8485b3f9..4fceb3f4c 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -334,7 +334,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { String extraArgs = "-L 1:1-10,000,000"; for (String tests : testsEnumerations) { WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s", - 1, Arrays.asList("b1cace2d6c5932a9a85f41fc10e607b4")); + 1, Arrays.asList("4ae87d76a3b39cf0b80221f3bd681839")); executeTestParallel("testSelect1", spec); //executeTest("testSelect1", 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 -ST CpG", "2a93c62ed4e062c043b7cc6dd0fa55f9"); - expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "aade8425705c8870adb9d3fd67cae555"); + expectations.put("-L 1:1-10,000,000 -ST CpG", "b82f1ad442d354a5ed3c18ecef93553e"); + expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "dc3d34f5a03890217d1f548027a82028"); for ( Map.Entry entry : expectations.entrySet() ) { String extraArgs = entry.getKey(); @@ -389,9 +389,9 @@ public class VariantEvalIntegrationTest extends WalkerTest { " -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf"; - expectations.put("", "fc552fc9a02ac0d2327d73c375aab45e"); - expectations.put(" -knownName comp_hapmap -knownName dbsnp", "09496523136290628bdc233f03ac9a38"); - expectations.put(" -knownName comp_hapmap", "8ad493a6427673ca6835303b41f40897"); + expectations.put("", "c3936ef2e7af52019ade05461fbf4180"); + expectations.put(" -knownName comp_hapmap -knownName dbsnp", "e19bd1bc89463e558fa3b83e65f55ca5"); + expectations.put(" -knownName comp_hapmap", "831d69ec830836f7d2ac8310713f1691"); for (String tests : testsEnumerations) { for (Map.Entry entry : expectations.entrySet()) { String extraArgs2 = entry.getKey(); @@ -409,7 +409,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testCompVsEvalAC() { 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("e83edc273504f5ea11de329f81af3de6")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("132e0825d1ed6e54963da94784cf7803")); executeTestParallel("testCompVsEvalAC",spec); //executeTest("testCompVsEvalAC",spec); } @@ -421,7 +421,7 @@ 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 -ST CpG -tf " + testDir + "tranches.6.txt"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("b018ca01b374def71fcd1bf164326485")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("4c5ef7c142427a85d1b9b1c9fe8fd3c2")); executeTestParallel("testTranches",spec); //executeTest("testTranches",spec); }