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Restored parallelism and associated tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5170 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-02-02 02:04:03 +00:00
parent fd8dd8fb9b
commit 2732c839d4
2 changed files with 20 additions and 16 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -652,7 +652,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
@Override @Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
for ( NewEvaluationContext nec : evaluationContexts.values() ) { for ( NewEvaluationContext nec : evaluationContexts.values() ) {
nec.update0(tracker, ref, context); synchronized (nec) {
nec.update0(tracker, ref, context);
}
} }
// track sample vc // track sample vc
@ -679,7 +681,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
for ( StateKey stateKey : stateKeysHash ) { for ( StateKey stateKey : stateKeysHash ) {
NewEvaluationContext nec = evaluationContexts.get(stateKey); NewEvaluationContext nec = evaluationContexts.get(stateKey);
nec.apply(tracker, ref, context, comp, eval); synchronized (nec) {
nec.apply(tracker, ref, context, comp, eval);
}
} }
} }
} }

28
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -30,8 +30,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
for (String tests : testsEnumerations) { 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 + " -o %s",
1, Arrays.asList("0087b2a096aa99135b065aa9a0fff34c")); 1, Arrays.asList("0087b2a096aa99135b065aa9a0fff34c"));
//executeTestParallel("testSelect1", spec); executeTestParallel("testSelect1", spec);
executeTest("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", WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
1, 1,
Arrays.asList("bb16335f9510bcab2bd14a4299afd879")); Arrays.asList("bb16335f9510bcab2bd14a4299afd879"));
//executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
executeTest("testVEGenotypeConcordance" + vcfFile, spec); //executeTest("testVEGenotypeConcordance" + vcfFile, spec);
} }
} }
@ -70,8 +70,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( tests + " " + extraArgs + " -o %s", WalkerTestSpec spec = new WalkerTestSpec( tests + " " + extraArgs + " -o %s",
1, // just one output file 1, // just one output file
Arrays.asList(md5)); Arrays.asList(md5));
//executeTestParallel("testVESimple", spec); executeTestParallel("testVESimple", spec);
executeTest("testVESimple", spec); //executeTest("testVESimple", spec);
} }
} }
} }
@ -96,8 +96,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs1 + extraArgs2 + " -o %s", WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs1 + extraArgs2 + " -o %s",
1, // just one output file 1, // just one output file
Arrays.asList(md5)); Arrays.asList(md5));
//executeTestParallel("testVEComplex", spec); executeTestParallel("testVEComplex", spec);
executeTest("testVEComplex", spec); //executeTest("testVEComplex", spec);
} }
} }
} }
@ -134,8 +134,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testCompVsEvalAC() { 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 -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")); WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("113228ffa35e0f67b8e067860c04171f"));
//executeTestParallel("testACDiscordanceAtAC1EvalAC2Comp",spec); executeTestParallel("testCompVsEvalAC",spec);
executeTest("testCompVsEvalAC",spec); //executeTest("testCompVsEvalAC",spec);
} }
private static String withSelect(String cmd, String select, String name) { private static String withSelect(String cmd, String select, String name) {
@ -146,16 +146,16 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testTranches() { 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 -tf " + testDir + "tranches.6.txt";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("68044a69f03ba4cc11d2061cc96e9eb5")); WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("68044a69f03ba4cc11d2061cc96e9eb5"));
//executeTestParallel("testTranches",spec); executeTestParallel("testTranches",spec);
executeTest("testTranches",spec); //executeTest("testTranches",spec);
} }
@Test @Test
public void testCompOverlap() { 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"; 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")); WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("81377be26bf8fa32339d01c173428f7d"));
//executeTestParallel("testTranches",spec); executeTestParallel("testCompOverlap",spec);
executeTest("testCompOverlap",spec); //executeTest("testCompOverlap",spec);
} }
// @Test // @Test