Updates to VariantEval 3.0 integration test.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5140 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran
parent
cab426f86f
commit
401feca90d
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@ -1,176 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.varianteval;
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import org.broadinstitute.sting.WalkerTest;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.testng.annotations.Test;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.Map;
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public class NewVariantEvalIntegrationTest extends WalkerTest {
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private static String cmdRoot = "-T NewVariantEval" +
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" -R " + b36KGReference;
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private static String root = cmdRoot +
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" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
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" -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
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" -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
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private static String rootGZ = cmdRoot +
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" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
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" -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
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" -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz";
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private static String[] testsEnumerations = {root, rootGZ};
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@Test
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public void testSelect1() {
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String extraArgs = "-L 1:1-10,000,000";
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for (String tests : testsEnumerations) {
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WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
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1, Arrays.asList("8ddc1c4a86cb3f4c22346497785b23e3"));
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//executeTestParallel("testSelect1", spec);
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executeTest("testSelect1", spec);
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}
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}
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// @Test
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// public void testSelect2() {
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// String extraArgs = "-L 1:1-10,000,000";
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// WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s",
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// 1, Arrays.asList(""));
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// //executeTestParallel("testSelect2", spec);
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// executeTest("testSelect2", spec);
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// }
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@Test
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public void testVEGenotypeConcordance() {
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String vcfFiles[] = {"GenotypeConcordanceEval.vcf", "GenotypeConcordanceEval.vcf.gz"};
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for (String vcfFile : vcfFiles) {
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WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
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1,
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Arrays.asList("7a6754176b573d14b6be7c808a04929d"));
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//executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
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executeTest("testVEGenotypeConcordance" + vcfFile, spec);
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}
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}
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@Test
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public void testVESimple() {
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HashMap<String, String> expectations = new HashMap<String, String>();
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expectations.put("-L 1:1-10,000,000", "ffd1abed44faf1590d9026e478b2f8ee");
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expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "32c2411fbf58bae5750c8229d15b98eb");
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for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
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String extraArgs = entry.getKey();
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String md5 = entry.getValue();
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for (String tests : testsEnumerations) {
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WalkerTestSpec spec = new WalkerTestSpec( tests + " " + extraArgs + " -o %s",
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1, // just one output file
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Arrays.asList(md5));
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//executeTestParallel("testVESimple", spec);
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executeTest("testVESimple", spec);
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}
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}
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}
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@Test
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public void testVEComplex() {
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HashMap<String, String> expectations = new HashMap<String, String>();
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String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator" +
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" -B:dbsnp_130,dbSNP " + GATKDataLocation + "dbsnp_130_b36.rod" +
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" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
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String matchingMD5 = "6c2fa6573cc57ef8795e9cce2b654d0b";
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expectations.put("", matchingMD5);
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expectations.put(" -knownName comp_hapmap -knownName dbsnp", matchingMD5);
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expectations.put(" -knownName comp_hapmap", "6c2fa6573cc57ef8795e9cce2b654d0b");
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for (String tests : testsEnumerations) {
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for (Map.Entry<String, String> entry : expectations.entrySet()) {
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String extraArgs2 = entry.getKey();
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String md5 = entry.getValue();
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WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs1 + extraArgs2 + " -o %s",
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1, // just one output file
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Arrays.asList(md5));
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//executeTestParallel("testVEComplex", spec);
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executeTest("testVEComplex", spec);
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}
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}
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}
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// @Test
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// public void testVEGenomicallyAnnotated() {
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// String vecmd = "-T NewVariantEval" +
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// " -R " + b36KGReference +
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// " -L 21" +
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// " -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
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// " -EV CountFunctionalClasses -noEV" +
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// " -B:eval,VCF " + validationDataLocation + "test.filtered.maf_annotated.vcf" +
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// " -o %s";
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// String md5 = "";
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//
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// WalkerTestSpec spec = new WalkerTestSpec(vecmd, 1, Arrays.asList(md5));
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// executeTestParallel("testVEGenomicallyAnnotated", spec);
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// //executeTest("testVEGenomicallyAnnotated", spec);
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// }
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//
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// @Test
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// public void testVEWriteVCF() {
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// String extraArgs = "-L 1:1-10,000,000 -NO_HEADER -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator";
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// for (String tests : testsEnumerations) {
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// WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s -NO_HEADER",
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// 2,
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// Arrays.asList("50321436a65ef7d574286cb0a1c55f7e", "d4bdd06ed5cb1aff1dfee8b69d5d17b8"));
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// executeTestParallel("testVEWriteVCF", spec);
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// //executeTest("testVEWriteVCF", spec);
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// }
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// }
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@Test
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public void testCompVsEvalAC() {
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String extraArgs = "-T NewVariantEval -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";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("929e4ec46fb6957c29803531322bb35e"));
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//executeTestParallel("testACDiscordanceAtAC1EvalAC2Comp",spec);
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executeTest("testCompVsEvalAC",spec);
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}
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private static String withSelect(String cmd, String select, String name) {
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return String.format("%s -select '%s' -selectName %s", cmd, select, name);
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}
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@Test
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public void testTranches() {
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String extraArgs = "-T NewVariantEval -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";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("68044a69f03ba4cc11d2061cc96e9eb5"));
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//executeTestParallel("testTranches",spec);
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executeTest("testTranches",spec);
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}
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// @Test
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// public void testVEValidatePass() {
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// String extraArgs = "-L 1:1-10,000,000";
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// for (String tests : testsEnumerations) {
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// WalkerTestSpec spec = new WalkerTestSpec(withValidateTiTv(withSelect(tests, "DP < 50", "DP50"), 1.0, 4.0) + " " + extraArgs + " -o %s",
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// 1, Arrays.asList("8a0203f0533b628ad7f1f230a43f105f"));
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// executeTestParallel("testVEValidatePass", spec);
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// }
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// }
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//
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// @Test
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// public void testVEValidateFail() {
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// String extraArgs = "-L 1:1-10,000,000";
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// for (String tests : testsEnumerations) {
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// WalkerTestSpec spec = new WalkerTestSpec(withValidateTiTv(withSelect(tests, "DP < 50", "DP50"), 1.0, 1.2) + " " + extraArgs + " -o %s",
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// 1, UserException.class);
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// executeTestParallel("testVEValidateFail", spec);
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// }
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// }
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//
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// private static String withValidateTiTv(String cmd, double min, double max) {
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// return String.format("%s -validate 'eval.comp_genotypes.all.called.all.titv.tiTvRatio >= %2$s' -validate 'eval.comp_genotypes.all.called.all.titv.tiTvRatio <= %3$s'", cmd, min, max);
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// }
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}
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@ -9,18 +9,18 @@ import java.util.HashMap;
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import java.util.Map;
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public class VariantEvalIntegrationTest extends WalkerTest {
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private static String cmdRoot = "-T VariantEval" +
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private static String cmdRoot = "-T NewVariantEval" +
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" -R " + b36KGReference;
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private static String root = cmdRoot +
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" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
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" -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
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" -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf -reportType Grep";
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" -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
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private static String rootGZ = cmdRoot +
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" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
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" -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
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" -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz -reportType Grep";
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" -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz";
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private static String[] testsEnumerations = {root, rootGZ};
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@ -29,30 +29,30 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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String extraArgs = "-L 1:1-10,000,000";
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for (String tests : testsEnumerations) {
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WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
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1, Arrays.asList("8a0203f0533b628ad7f1f230a43f105f"));
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executeTestParallel("testSelect1", spec);
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//executeTest("testSelect1", spec);
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1, Arrays.asList("8ddc1c4a86cb3f4c22346497785b23e3"));
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//executeTestParallel("testSelect1", spec);
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executeTest("testSelect1", spec);
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}
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}
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@Test
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public void testSelect2() {
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String extraArgs = "-L 1:1-10,000,000";
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WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s",
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1, Arrays.asList("a55653980b750fdc8396eecb00e3b18c"));
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executeTestParallel("testSelect2", spec);
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//executeTest("testSelect2", spec);
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}
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// @Test
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// public void testSelect2() {
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// String extraArgs = "-L 1:1-10,000,000";
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// WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s",
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// 1, Arrays.asList(""));
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// //executeTestParallel("testSelect2", spec);
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// executeTest("testSelect2", spec);
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// }
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@Test
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public void testVEGenotypeConcordance() {
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String vcfFiles[] = {"GenotypeConcordanceEval.vcf", "GenotypeConcordanceEval.vcf.gz"};
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for (String vcfFile : vcfFiles) {
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WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noStandard -E GenotypeConcordance -reportType CSV -o %s",
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WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
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1,
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Arrays.asList("7e9ce1b26cdeaa50705f5de163847638"));
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executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
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//executeTest("testVEGenotypeConcordance" + vcfFile, spec);
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Arrays.asList("7a6754176b573d14b6be7c808a04929d"));
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//executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
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executeTest("testVEGenotypeConcordance" + vcfFile, spec);
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}
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}
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@ -60,8 +60,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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@Test
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public void testVESimple() {
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HashMap<String, String> expectations = new HashMap<String, String>();
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expectations.put("-L 1:1-10,000,000", "6c9a12fdd62672b69b2ed4f0bc7e8f97");
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expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0 -E MendelianViolationEvaluator", "6a52a6454121974b71d9cfe2dad68c28");
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expectations.put("-L 1:1-10,000,000", "ffd1abed44faf1590d9026e478b2f8ee");
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expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "32c2411fbf58bae5750c8229d15b98eb");
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for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
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String extraArgs = entry.getKey();
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@ -70,8 +70,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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WalkerTestSpec spec = new WalkerTestSpec( tests + " " + extraArgs + " -o %s",
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1, // just one output file
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Arrays.asList(md5));
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executeTestParallel("testVESimple", spec);
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//executeTest("testVESimple", spec);
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//executeTestParallel("testVESimple", spec);
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executeTest("testVESimple", spec);
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}
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}
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}
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@ -79,15 +79,15 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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@Test
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public void testVEComplex() {
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HashMap<String, String> expectations = new HashMap<String, String>();
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String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -MVQ 30 -E MendelianViolationEvaluator" +
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String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator" +
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" -B:dbsnp_130,dbSNP " + GATKDataLocation + "dbsnp_130_b36.rod" +
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" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
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String matchingMD5 = "7a8183402fe29f9c62c3c3cc4d45b46e";
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String matchingMD5 = "6c2fa6573cc57ef8795e9cce2b654d0b";
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expectations.put("", matchingMD5);
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expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5);
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expectations.put(" -known comp_hapmap", "519b590635b7de035f8d5971115b47ba");
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expectations.put(" -knownName comp_hapmap -knownName dbsnp", matchingMD5);
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expectations.put(" -knownName comp_hapmap", "6c2fa6573cc57ef8795e9cce2b654d0b");
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for (String tests : testsEnumerations) {
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for (Map.Entry<String, String> entry : expectations.entrySet()) {
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String extraArgs2 = entry.getKey();
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@ -96,46 +96,46 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs1 + extraArgs2 + " -o %s",
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1, // just one output file
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Arrays.asList(md5));
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executeTestParallel("testVEComplex", spec);
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//executeTest("testVEComplex", spec);
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//executeTestParallel("testVEComplex", spec);
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executeTest("testVEComplex", spec);
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}
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}
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}
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@Test
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public void testVEGenomicallyAnnotated() {
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String vecmd = "-T VariantEval" +
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" -R " + b36KGReference +
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" -L 21" +
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" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
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" -E CountFunctionalClasses -noStandard" +
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" -B:eval,VCF " + validationDataLocation + "test.filtered.maf_annotated.vcf" +
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" -o %s";
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String md5 = "d41d8cd98f00b204e9800998ecf8427e";
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WalkerTestSpec spec = new WalkerTestSpec(vecmd, 1, Arrays.asList(md5));
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executeTestParallel("testVEGenomicallyAnnotated", spec);
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//executeTest("testVEGenomicallyAnnotated", spec);
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}
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@Test
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public void testVEWriteVCF() {
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String extraArgs = "-L 1:1-10,000,000 -NO_HEADER -family NA19238+NA19239=NA19240 -MVQ 30 -E MendelianViolationEvaluator";
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for (String tests : testsEnumerations) {
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WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s -NO_HEADER",
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2,
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Arrays.asList("50321436a65ef7d574286cb0a1c55f7e", "d4bdd06ed5cb1aff1dfee8b69d5d17b8"));
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executeTestParallel("testVEWriteVCF", spec);
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//executeTest("testVEWriteVCF", spec);
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}
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}
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// @Test
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// public void testVEGenomicallyAnnotated() {
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// String vecmd = "-T NewVariantEval" +
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// " -R " + b36KGReference +
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// " -L 21" +
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// " -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
|
||||
// " -EV CountFunctionalClasses -noEV" +
|
||||
// " -B:eval,VCF " + validationDataLocation + "test.filtered.maf_annotated.vcf" +
|
||||
// " -o %s";
|
||||
// String md5 = "";
|
||||
//
|
||||
// WalkerTestSpec spec = new WalkerTestSpec(vecmd, 1, Arrays.asList(md5));
|
||||
// executeTestParallel("testVEGenomicallyAnnotated", spec);
|
||||
// //executeTest("testVEGenomicallyAnnotated", spec);
|
||||
// }
|
||||
//
|
||||
// @Test
|
||||
// public void testVEWriteVCF() {
|
||||
// String extraArgs = "-L 1:1-10,000,000 -NO_HEADER -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator";
|
||||
// for (String tests : testsEnumerations) {
|
||||
// WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s -NO_HEADER",
|
||||
// 2,
|
||||
// Arrays.asList("50321436a65ef7d574286cb0a1c55f7e", "d4bdd06ed5cb1aff1dfee8b69d5d17b8"));
|
||||
// executeTestParallel("testVEWriteVCF", spec);
|
||||
// //executeTest("testVEWriteVCF", spec);
|
||||
// }
|
||||
// }
|
||||
|
||||
@Test
|
||||
public void testCompVsEvalAC() {
|
||||
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -E 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 -reportType CSV";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("25a681855cb26e7380fbf1a93de0a41f"));
|
||||
executeTestParallel("testACDiscordanceAtAC1EvalAC2Comp",spec);
|
||||
//executeTest("testACDiscordanceAtAC1EvalAC2Comp",spec);
|
||||
String extraArgs = "-T NewVariantEval -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("929e4ec46fb6957c29803531322bb35e"));
|
||||
//executeTestParallel("testACDiscordanceAtAC1EvalAC2Comp",spec);
|
||||
executeTest("testCompVsEvalAC",spec);
|
||||
}
|
||||
|
||||
private static String withSelect(String cmd, String select, String name) {
|
||||
|
|
@ -144,33 +144,33 @@ 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 -E TiTvVariantEvaluator -L chr1 -noStandard -reportType CSV -tf " + testDir + "tranches.6.txt";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("1002c7a71e6c14f87398d924ac1d92af"));
|
||||
executeTestParallel("testTranches",spec);
|
||||
//executeTest("testACDiscordanceAtAC1EvalAC2Comp",spec);
|
||||
String extraArgs = "-T NewVariantEval -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);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testVEValidatePass() {
|
||||
String extraArgs = "-L 1:1-10,000,000";
|
||||
for (String tests : testsEnumerations) {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(withValidateTiTv(withSelect(tests, "DP < 50", "DP50"), 1.0, 4.0) + " " + extraArgs + " -o %s",
|
||||
1, Arrays.asList("8a0203f0533b628ad7f1f230a43f105f"));
|
||||
executeTestParallel("testVEValidatePass", spec);
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testVEValidateFail() {
|
||||
String extraArgs = "-L 1:1-10,000,000";
|
||||
for (String tests : testsEnumerations) {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(withValidateTiTv(withSelect(tests, "DP < 50", "DP50"), 1.0, 1.2) + " " + extraArgs + " -o %s",
|
||||
1, UserException.class);
|
||||
executeTestParallel("testVEValidateFail", spec);
|
||||
}
|
||||
}
|
||||
|
||||
private static String withValidateTiTv(String cmd, double min, double max) {
|
||||
return String.format("%s -validate 'eval.comp_genotypes.all.called.all.titv.tiTvRatio >= %2$s' -validate 'eval.comp_genotypes.all.called.all.titv.tiTvRatio <= %3$s'", cmd, min, max);
|
||||
}
|
||||
// @Test
|
||||
// public void testVEValidatePass() {
|
||||
// String extraArgs = "-L 1:1-10,000,000";
|
||||
// for (String tests : testsEnumerations) {
|
||||
// WalkerTestSpec spec = new WalkerTestSpec(withValidateTiTv(withSelect(tests, "DP < 50", "DP50"), 1.0, 4.0) + " " + extraArgs + " -o %s",
|
||||
// 1, Arrays.asList("8a0203f0533b628ad7f1f230a43f105f"));
|
||||
// executeTestParallel("testVEValidatePass", spec);
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// @Test
|
||||
// public void testVEValidateFail() {
|
||||
// String extraArgs = "-L 1:1-10,000,000";
|
||||
// for (String tests : testsEnumerations) {
|
||||
// WalkerTestSpec spec = new WalkerTestSpec(withValidateTiTv(withSelect(tests, "DP < 50", "DP50"), 1.0, 1.2) + " " + extraArgs + " -o %s",
|
||||
// 1, UserException.class);
|
||||
// executeTestParallel("testVEValidateFail", spec);
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// private static String withValidateTiTv(String cmd, double min, double max) {
|
||||
// return String.format("%s -validate 'eval.comp_genotypes.all.called.all.titv.tiTvRatio >= %2$s' -validate 'eval.comp_genotypes.all.called.all.titv.tiTvRatio <= %3$s'", cmd, min, max);
|
||||
// }
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue