diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/NewVariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/NewVariantEvalIntegrationTest.java deleted file mode 100755 index 21a80e508..000000000 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/NewVariantEvalIntegrationTest.java +++ /dev/null @@ -1,176 +0,0 @@ -package org.broadinstitute.sting.gatk.walkers.varianteval; - -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.testng.annotations.Test; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.Map; - -public class NewVariantEvalIntegrationTest extends WalkerTest { - private static String cmdRoot = "-T NewVariantEval" + - " -R " + b36KGReference; - - private static String root = cmdRoot + - " -D " + GATKDataLocation + "dbsnp_129_b36.rod" + - " -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + - " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; - - private static String rootGZ = cmdRoot + - " -D " + GATKDataLocation + "dbsnp_129_b36.rod" + - " -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" + - " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz"; - - private static String[] testsEnumerations = {root, rootGZ}; - - @Test - 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", - 1, Arrays.asList("8ddc1c4a86cb3f4c22346497785b23e3")); - //executeTestParallel("testSelect1", spec); - executeTest("testSelect1", spec); - } - } - -// @Test -// public void testSelect2() { -// String extraArgs = "-L 1:1-10,000,000"; -// WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s", -// 1, Arrays.asList("")); -// //executeTestParallel("testSelect2", spec); -// executeTest("testSelect2", spec); -// } - - @Test - 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", - 1, - Arrays.asList("7a6754176b573d14b6be7c808a04929d")); - //executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); - executeTest("testVEGenotypeConcordance" + vcfFile, spec); - } - - } - - @Test - public void testVESimple() { - HashMap expectations = new HashMap(); - expectations.put("-L 1:1-10,000,000", "ffd1abed44faf1590d9026e478b2f8ee"); - expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "32c2411fbf58bae5750c8229d15b98eb"); - - for ( Map.Entry entry : expectations.entrySet() ) { - String extraArgs = entry.getKey(); - String md5 = entry.getValue(); - for (String tests : testsEnumerations) { - WalkerTestSpec spec = new WalkerTestSpec( tests + " " + extraArgs + " -o %s", - 1, // just one output file - Arrays.asList(md5)); - //executeTestParallel("testVESimple", spec); - executeTest("testVESimple", spec); - } - } - } - - @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" + - " -B:dbsnp_130,dbSNP " + GATKDataLocation + "dbsnp_130_b36.rod" + - " -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf"; - - - String matchingMD5 = "6c2fa6573cc57ef8795e9cce2b654d0b"; - expectations.put("", matchingMD5); - expectations.put(" -knownName comp_hapmap -knownName dbsnp", matchingMD5); - expectations.put(" -knownName comp_hapmap", "6c2fa6573cc57ef8795e9cce2b654d0b"); - for (String tests : testsEnumerations) { - for (Map.Entry entry : expectations.entrySet()) { - String extraArgs2 = entry.getKey(); - String md5 = entry.getValue(); - - WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs1 + extraArgs2 + " -o %s", - 1, // just one output file - Arrays.asList(md5)); - //executeTestParallel("testVEComplex", spec); - executeTest("testVEComplex", spec); - } - } - } - -// @Test -// public void testVEGenomicallyAnnotated() { -// String vecmd = "-T NewVariantEval" + -// " -R " + b36KGReference + -// " -L 21" + -// " -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 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) { - return String.format("%s -select '%s' -selectName %s", cmd, select, name); - } - - @Test - public void testTranches() { - 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); -// } -} 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 ec0206aac..52153d1be 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -9,18 +9,18 @@ import java.util.HashMap; import java.util.Map; public class VariantEvalIntegrationTest extends WalkerTest { - private static String cmdRoot = "-T VariantEval" + + private static String cmdRoot = "-T NewVariantEval" + " -R " + b36KGReference; private static String root = cmdRoot + " -D " + GATKDataLocation + "dbsnp_129_b36.rod" + " -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + - " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf -reportType Grep"; + " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; private static String rootGZ = cmdRoot + " -D " + GATKDataLocation + "dbsnp_129_b36.rod" + " -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" + - " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz -reportType Grep"; + " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz"; private static String[] testsEnumerations = {root, rootGZ}; @@ -29,30 +29,30 @@ 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 + " -o %s", - 1, Arrays.asList("8a0203f0533b628ad7f1f230a43f105f")); - executeTestParallel("testSelect1", spec); - //executeTest("testSelect1", spec); + 1, Arrays.asList("8ddc1c4a86cb3f4c22346497785b23e3")); + //executeTestParallel("testSelect1", spec); + executeTest("testSelect1", spec); } } - @Test - public void testSelect2() { - String extraArgs = "-L 1:1-10,000,000"; - WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s", - 1, Arrays.asList("a55653980b750fdc8396eecb00e3b18c")); - executeTestParallel("testSelect2", spec); - //executeTest("testSelect2", spec); - } +// @Test +// public void testSelect2() { +// String extraArgs = "-L 1:1-10,000,000"; +// WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s", +// 1, Arrays.asList("")); +// //executeTestParallel("testSelect2", spec); +// executeTest("testSelect2", spec); +// } @Test 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 -noStandard -E GenotypeConcordance -reportType CSV -o %s", + WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", 1, - Arrays.asList("7e9ce1b26cdeaa50705f5de163847638")); - executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); - //executeTest("testVEGenotypeConcordance" + vcfFile, spec); + Arrays.asList("7a6754176b573d14b6be7c808a04929d")); + //executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); + executeTest("testVEGenotypeConcordance" + vcfFile, spec); } } @@ -60,8 +60,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testVESimple() { HashMap expectations = new HashMap(); - expectations.put("-L 1:1-10,000,000", "6c9a12fdd62672b69b2ed4f0bc7e8f97"); - expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0 -E MendelianViolationEvaluator", "6a52a6454121974b71d9cfe2dad68c28"); + expectations.put("-L 1:1-10,000,000", "ffd1abed44faf1590d9026e478b2f8ee"); + expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "32c2411fbf58bae5750c8229d15b98eb"); for ( Map.Entry entry : expectations.entrySet() ) { String extraArgs = entry.getKey(); @@ -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); } } } @@ -79,15 +79,15 @@ 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 -E MendelianViolationEvaluator" + + String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator" + " -B:dbsnp_130,dbSNP " + GATKDataLocation + "dbsnp_130_b36.rod" + " -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf"; - String matchingMD5 = "7a8183402fe29f9c62c3c3cc4d45b46e"; + String matchingMD5 = "6c2fa6573cc57ef8795e9cce2b654d0b"; expectations.put("", matchingMD5); - expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5); - expectations.put(" -known comp_hapmap", "519b590635b7de035f8d5971115b47ba"); + expectations.put(" -knownName comp_hapmap -knownName dbsnp", matchingMD5); + expectations.put(" -knownName comp_hapmap", "6c2fa6573cc57ef8795e9cce2b654d0b"); for (String tests : testsEnumerations) { for (Map.Entry entry : expectations.entrySet()) { String extraArgs2 = entry.getKey(); @@ -96,46 +96,46 @@ 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); } } } - @Test - public void testVEGenomicallyAnnotated() { - String vecmd = "-T VariantEval" + - " -R " + b36KGReference + - " -L 21" + - " -D " + GATKDataLocation + "dbsnp_129_b36.rod" + - " -E CountFunctionalClasses -noStandard" + - " -B:eval,VCF " + validationDataLocation + "test.filtered.maf_annotated.vcf" + - " -o %s"; - String md5 = "d41d8cd98f00b204e9800998ecf8427e"; - - 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 -E 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 testVEGenomicallyAnnotated() { +// String vecmd = "-T NewVariantEval" + +// " -R " + b36KGReference + +// " -L 21" + +// " -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); +// } }