diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index 3522e3a8d..3e4637b7f 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/GaussianMixtureModel.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java index 58f05633d..9ffe7be7a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/GaussianMixtureModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import Jama.Matrix; import cern.jet.random.Normal; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/MultivariateGaussian.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/MultivariateGaussian.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java index 78935fb2d..52402ad8a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/MultivariateGaussian.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import Jama.Matrix; import org.apache.commons.math.special.Gamma; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrainingSet.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java similarity index 94% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrainingSet.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java index e9c67a21e..f3677421e 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrainingSet.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.Tags; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/Tranche.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/Tranche.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java index b685c9e68..1ca905518 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/Tranche.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java index 3bae46247..08388db21 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java index b1f6596cb..4ebe9807b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; import org.broad.tribble.util.variantcontext.VariantContext; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDataManager.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java index fd7a548d1..3c4985d92 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import cern.jet.random.Normal; import org.apache.log4j.Logger; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDatum.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java similarity index 91% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDatum.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java index 2509bba1e..08e44f6cf 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDatum.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index 631453656..b9ff68641 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.commandline.Argument; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java index bd1d030bb..7a524f259 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.broadinstitute.sting.commandline.Argument; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java rename to java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java index b3284efc4..e87048a13 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; +package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index 60c891f5e..b44615c6b 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -1,12 +1,10 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.annotations.Test; import org.testng.annotations.DataProvider; import java.util.*; -import java.io.File; public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { static HashMap clusterFiles = new HashMap(); @@ -15,111 +13,61 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { private static class VRTest { String inVCF; - String clusterMD5; String tranchesMD5; - String recalVCFMD5; + String recalMD5; String cutVCFMD5; - public VRTest(String inVCF, String clusterMD5, String tranchesMD5, String recalVCFMD5, String cutVCFMD5) { + public VRTest(String inVCF, String tranchesMD5, String recalMD5, String cutVCFMD5) { this.inVCF = validationDataLocation + inVCF; - this.clusterMD5 = clusterMD5; this.tranchesMD5 = tranchesMD5; - this.recalVCFMD5 = recalVCFMD5; + this.recalMD5 = recalMD5; this.cutVCFMD5 = cutVCFMD5; } } - VRTest yriTrio = new VRTest("yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", - "f65c27ee40053adc72dd0bfbb628e4d7", // cluster file - "dce581b880ffb6ea39cbada1ecc95915", // tranches - "c3e8a2f43656eab7d847dbf850f844a6", // recalVCF - "50f752a72643db9ad0aa94b3fc4e23d6"); // cut VCF - - VRTest lowPass = new VRTest("lowpass.N3.chr1.raw.vcf", - "bda8f17cfc19d23e7e51f99e547f4b3d", // cluster file - "66edae83c50f4e8601fef7fafba774af", // tranches - "0123537e373657386068a534c0f5c91b", // recalVCF - "2172368e8585841e5ad96c95d0827c4b"); // cut VCF + VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf", + "920b12d7765eb4f6f4a1bab045679b31", // tranches + "41bbc5f07c8a9573d5bb638f01808bba", // recal file + "d9aa7a0f8fb886df4394f1636605adca"); // cut VCF @DataProvider(name = "VRTest") public Object[][] createData1() { - return new Object[][]{ {yriTrio}, {lowPass} }; + return new Object[][]{ {lowPass} }; + //return new Object[][]{ {yriTrio}, {lowPass} }; // Add hg19 chr20 trio calls here } - @Test(dataProvider = "VRTest", enabled = true) - public void testGenerateVariantClusters(VRTest params) { - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + b36KGReference + - " -NO_HEADER" + - " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" + - " -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/sites_r27_nr.b36_fwd.vcf" + - " -weightDBSNP 1.0 -weightHapMap 1.0" + - " -T GenerateVariantClusters" + - " -B:input,VCF " + params.inVCF + - " -L 1:50,000,000-200,000,000" + - " -qual 50.0" + - " --ignore_filter GATK_STANDARD" + - " -an QD -an MQ -an SB" + - " -clusterFile %s", - Arrays.asList(params.clusterMD5)); - executeTest("testGenerateVariantClusters-"+params.inVCF, spec).getFirst(); - } - - @Test(dataProvider = "VRTest",dependsOnMethods="testGenerateVariantClusters") + @Test(dataProvider = "VRTest") public void testVariantRecalibrator(VRTest params) { //System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + b36KGReference + - " -NO_HEADER" + - " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" + - " -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/sites_r27_nr.b36_fwd.vcf" + - " -B:truthHapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/sites_r27_nr.b36_fwd.vcf" + + "-R " + b37KGReference + + " -B:dbsnp,VCF,known=true,training=false,truth=false,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" + + " -B:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" + + " -B:omni,VCF,known=false,training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" + " -T VariantRecalibrator" + " -B:input,VCF " + params.inVCF + - " -L 1:20,000,000-100,000,000" + - " --ignore_filter GATK_STANDARD" + - " --ignore_filter HARD_TO_VALIDATE" + - " -clusterFile " + getFileForMD5(params.clusterMD5) + - " -sm TRUTH_SENSITIVITY" + - " -o %s" + + " -L 20:1,000,000-40,000,000" + + " -an QD -an HaplotypeScore -an HRun" + + " -percentBad 0.07" + + " --trustAllPolymorphic" + // for speed + " -recalFile %s" + " -tranchesFile %s", - Arrays.asList(params.recalVCFMD5, params.tranchesMD5)); + Arrays.asList(params.recalMD5, params.tranchesMD5)); executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst(); } @Test(dataProvider = "VRTest",dependsOnMethods="testVariantRecalibrator") - public void testApplyVariantCuts(VRTest params) { + public void testApplyRecalibration(VRTest params) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + b36KGReference + + "-R " + b37KGReference + + " -T ApplyRecalibration" + + " -L 20:12,000,000-30,000,000" + " -NO_HEADER" + - " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" + - " -T ApplyVariantCuts" + - " -L 1:20,000,000-100,000,000" + - " -B:input,VCF " + getFileForMD5(params.recalVCFMD5) + + " -B:input,VCF " + params.inVCF + " -o %s" + - " -tranchesFile " + getFileForMD5(params.tranchesMD5), + " -tranchesFile " + getFileForMD5(params.tranchesMD5) + + " -recalFile " + getFileForMD5(params.recalMD5), Arrays.asList(params.cutVCFMD5)); - executeTest("testApplyVariantCuts-"+params.inVCF, spec); - } - - - @Test() - public void testFailWithBadAnnotation() { - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + b36KGReference + - " -NO_HEADER" + - " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" + - " -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/sites_r27_nr.b36_fwd.vcf" + - " -weightDBSNP 0.2 -weightHapMap 1.0" + - " -T GenerateVariantClusters" + - " -B:input,VCF " + lowPass.inVCF + - " -L 1:50,000,000-200,000,000" + - " -qual 50.0" + - " --ignore_filter GATK_STANDARD" + - " -an QD -an HRun -an ThisAnnotationIsBAD" + // There is a bad annotation here - " -clusterFile %s", - 1, // just one output file - UserException.MalformedFile.class); - executeTest("testFailWithBadAnnotation", spec); + executeTest("testApplyRecalibration-"+params.inVCF, spec); } } diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java deleted file mode 100755 index da00b6ee9..000000000 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java +++ /dev/null @@ -1,73 +0,0 @@ -package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration; - -import org.broadinstitute.sting.WalkerTest; -import org.testng.annotations.Test; -import org.testng.annotations.DataProvider; - -import java.util.*; - -public class VariantRecalibrationWalkersV2IntegrationTest extends WalkerTest { - static HashMap clusterFiles = new HashMap(); - static HashMap tranchesFiles = new HashMap(); - static HashMap inputVCFFiles = new HashMap(); - - private static class VRTest { - String inVCF; - String tranchesMD5; - String recalMD5; - String cutVCFMD5; - public VRTest(String inVCF, String tranchesMD5, String recalMD5, String cutVCFMD5) { - this.inVCF = validationDataLocation + inVCF; - this.tranchesMD5 = tranchesMD5; - this.recalMD5 = recalMD5; - this.cutVCFMD5 = cutVCFMD5; - } - } - - VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf", - "920b12d7765eb4f6f4a1bab045679b31", // tranches - "41bbc5f07c8a9573d5bb638f01808bba", // recal file - "d9aa7a0f8fb886df4394f1636605adca"); // cut VCF - - @DataProvider(name = "VRTest") - public Object[][] createData1() { - return new Object[][]{ {lowPass} }; - //return new Object[][]{ {yriTrio}, {lowPass} }; // Add hg19 chr20 trio calls here - } - - @Test(dataProvider = "VRTest") - public void testVariantRecalibrator(VRTest params) { - //System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile); - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + b37KGReference + - " -B:dbsnp,VCF,known=true,training=false,truth=false,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" + - " -B:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" + - " -B:omni,VCF,known=false,training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" + - " -T VariantRecalibrator" + - " -B:input,VCF " + params.inVCF + - " -L 20:1,000,000-40,000,000" + - " -an QD -an HaplotypeScore -an HRun" + - " -percentBad 0.07" + - " --trustAllPolymorphic" + // for speed - " -recalFile %s" + - " -tranchesFile %s", - Arrays.asList(params.recalMD5, params.tranchesMD5)); - executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst(); - } - - @Test(dataProvider = "VRTest",dependsOnMethods="testVariantRecalibrator") - public void testApplyRecalibration(VRTest params) { - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + b37KGReference + - " -T ApplyRecalibration" + - " -L 20:12,000,000-30,000,000" + - " -NO_HEADER" + - " -B:input,VCF " + params.inVCF + - " -o %s" + - " -tranchesFile " + getFileForMD5(params.tranchesMD5) + - " -recalFile " + getFileForMD5(params.recalMD5), - Arrays.asList(params.cutVCFMD5)); - executeTest("testApplyRecalibration-"+params.inVCF, spec); - } -} -