From 2732c839d4a406bcc524e3a469f470ff8d76ec28 Mon Sep 17 00:00:00 2001 From: kiran Date: Wed, 2 Feb 2011 02:04:03 +0000 Subject: [PATCH] Restored parallelism and associated tests. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5170 348d0f76-0448-11de-a6fe-93d51630548a --- .../varianteval/VariantEvalWalker.java | 8 ++++-- .../VariantEvalIntegrationTest.java | 28 +++++++++---------- 2 files changed, 20 insertions(+), 16 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 61d61581a..5ea63504b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -652,7 +652,9 @@ public class VariantEvalWalker extends RodWalker implements Tr @Override public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { for ( NewEvaluationContext nec : evaluationContexts.values() ) { - nec.update0(tracker, ref, context); + synchronized (nec) { + nec.update0(tracker, ref, context); + } } // track sample vc @@ -679,7 +681,9 @@ public class VariantEvalWalker extends RodWalker implements Tr for ( StateKey stateKey : stateKeysHash ) { NewEvaluationContext nec = evaluationContexts.get(stateKey); - nec.apply(tracker, ref, context, comp, eval); + synchronized (nec) { + nec.apply(tracker, ref, context, comp, eval); + } } } } 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 840accea8..972dcf22e 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -30,8 +30,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { for (String tests : testsEnumerations) { WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s", 1, Arrays.asList("0087b2a096aa99135b065aa9a0fff34c")); - //executeTestParallel("testSelect1", spec); - executeTest("testSelect1", spec); + executeTestParallel("testSelect1", spec); + //executeTest("testSelect1", spec); } } @@ -51,8 +51,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", 1, Arrays.asList("bb16335f9510bcab2bd14a4299afd879")); - //executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); - executeTest("testVEGenotypeConcordance" + vcfFile, spec); + executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); + //executeTest("testVEGenotypeConcordance" + vcfFile, spec); } } @@ -70,8 +70,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( tests + " " + extraArgs + " -o %s", 1, // just one output file Arrays.asList(md5)); - //executeTestParallel("testVESimple", spec); - executeTest("testVESimple", spec); + executeTestParallel("testVESimple", spec); + //executeTest("testVESimple", spec); } } } @@ -96,8 +96,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs1 + extraArgs2 + " -o %s", 1, // just one output file Arrays.asList(md5)); - //executeTestParallel("testVEComplex", spec); - executeTest("testVEComplex", spec); + executeTestParallel("testVEComplex", spec); + //executeTest("testVEComplex", spec); } } } @@ -134,8 +134,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { 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"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("113228ffa35e0f67b8e067860c04171f")); - //executeTestParallel("testACDiscordanceAtAC1EvalAC2Comp",spec); - executeTest("testCompVsEvalAC",spec); + executeTestParallel("testCompVsEvalAC",spec); + //executeTest("testCompVsEvalAC",spec); } private static String withSelect(String cmd, String select, String name) { @@ -146,16 +146,16 @@ public class VariantEvalIntegrationTest extends WalkerTest { 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"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("68044a69f03ba4cc11d2061cc96e9eb5")); - //executeTestParallel("testTranches",spec); - executeTest("testTranches",spec); + executeTestParallel("testTranches",spec); + //executeTest("testTranches",spec); } @Test public void testCompOverlap() { String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals -B:comphapmap,vcf " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf -B:eval,vcf " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("81377be26bf8fa32339d01c173428f7d")); - //executeTestParallel("testTranches",spec); - executeTest("testCompOverlap",spec); + executeTestParallel("testCompOverlap",spec); + //executeTest("testCompOverlap",spec); } // @Test