diff --git a/build.gradle b/build.gradle index a3781be03d3..711cf117f72 100644 --- a/build.gradle +++ b/build.gradle @@ -182,8 +182,19 @@ compileTestJava { options.compilerArgs = ['-proc:none', '-Xlint:all', '-Werror', '-Xdiags:verbose'] } + +sourceSets { + testUtils +} + // Dependency change for including MLLib configurations { + testUtilsCompile.extendsFrom compile + testUtilsRuntime.extendsFrom runtime + + testCompile.extendsFrom testUtilsCompile + testRuntime.extendsFrom testUtilsRuntime + compile.exclude module: 'jul-to-slf4j' compile.exclude module: 'javax.servlet' compile.exclude module: 'servlet-api' @@ -279,8 +290,6 @@ dependencies { } compile 'org.jgrapht:jgrapht-core:0.9.1' - compile 'org.testng:testng:' + testNGVersion //compile instead of testCompile because it is needed for test infrastructure that needs to be packaged - compile 'org.apache.hadoop:hadoop-minicluster:' + hadoopVersion compile('org.seqdoop:hadoop-bam:' + hadoopBamVersion) { exclude group: 'org.apache.hadoop' @@ -325,6 +334,12 @@ dependencies { // Required for SV Discovery machine learning compile group: 'biz.k11i', name: 'xgboost-predictor', version: '0.3.0' + testUtilsCompile sourceSets.main.output + testUtilsCompile 'org.testng:testng:' + testNGVersion + testUtilsCompile 'org.apache.hadoop:hadoop-minicluster:' + hadoopVersion + + testCompile sourceSets.testUtils.output + testCompile "org.mockito:mockito-core:2.10.0" testCompile "com.google.jimfs:jimfs:1.1" } @@ -677,6 +692,11 @@ task sourcesJar(type: Jar) { classifier = 'sources' } +task testUtilsJar(type: Jar){ + baseName = "$project.name-test-utils" + from sourceSets.testUtils.output +} + tasks.withType(Javadoc) { // do this for all javadoc tasks, including gatkDoc options.addStringOption('Xdoclint:none') @@ -690,6 +710,29 @@ javadoc { include '**/*.java' } + +task testUtilsJavadoc(type: Javadoc) { + // This is a hack to disable the java 8 default javadoc lint until we fix the html formatting + // We only want to do this for the javadoc task, not gatkDoc + options.addStringOption('Xdoclint:none', '-quiet') + source = sourceSets.testUtils.allJava + classpath = sourceSets.testUtils.runtimeClasspath + destinationDir = file("$docBuildDir/testUtilsJavadoc") + include '**/*.java' +} + +task testUtilsJavadocJar(type: Jar, dependsOn: testUtilsJavadoc){ + baseName = "$project.name-test-utils" + classifier = 'javadoc' + from "$docBuildDir/testUtilsJavadoc" +} + +task testUtilsSourceJar(type: Jar){ + baseName = "$project.name-test-utils" + classifier = 'source' + from sourceSets.testUtils.allSource +} + // Generate GATK Online Doc task gatkDoc(type: Javadoc, dependsOn: classes) { final File gatkDocDir = new File("$docBuildDir/gatkdoc") @@ -782,6 +825,8 @@ task gatkTabComplete(type: Javadoc, dependsOn: classes) { options.addStringOption("caller-post-arg-max-occurs", "1 1 1 1 1 1 1 1 1 1") } + + /** *This specifies what artifacts will be built and uploaded when performing a maven upload. */ @@ -789,6 +834,9 @@ artifacts { archives jar archives javadocJar archives sourcesJar + archives testUtilsJar + archives testUtilsJavadocJar + archives testUtilsSourceJar } //remove zip and tar added by the application plugin @@ -803,6 +851,17 @@ signing { sign configurations.archives } +def gatkArtifactFilter = { artifact, file -> artifact.name == 'gatk' } +def gatkTestUtilsArtifactFilter = {artifact, file -> artifact.name == 'gatk-test-utils' } + +install { + install { + repositories.mavenInstaller { + addFilter('gatk', gatkArtifactFilter) + addFilter('gatk-test-utils', gatkTestUtilsArtifactFilter) + } + } +} /** * Upload a release to sonatype. You must be an authorized uploader and have your sonatype * username and password information in your gradle properties file. See the readme for more info. @@ -825,6 +884,9 @@ uploadArchives { authentication(userName: System.env.ARTIFACTORY_USERNAME, password: System.env.ARTIFACTORY_PASSWORD) } + addFilter('gatk', gatkArtifactFilter) + addFilter('gatk-test-utils', gatkTestUtilsArtifactFilter) + pom.project { name 'GATK4' packaging 'jar' diff --git a/src/main/java/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart.java b/src/main/java/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart.java index f425d290b2c..03733e9af7e 100644 --- a/src/main/java/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart.java +++ b/src/main/java/org/broadinstitute/hellbender/engine/MultiVariantWalkerGroupedOnStart.java @@ -3,18 +3,13 @@ import com.google.common.annotations.VisibleForTesting; import htsjdk.samtools.util.Locatable; import htsjdk.samtools.util.OverlapDetector; -import htsjdk.variant.variantcontext.Allele; -import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; -import htsjdk.variant.variantcontext.VariantContextBuilder; import org.broadinstitute.barclay.argparser.Advanced; import org.broadinstitute.barclay.argparser.Argument; -import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; -import java.util.*; +import java.util.ArrayList; +import java.util.List; /** diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java index 1a9d70ad6c3..6c5a97d95a2 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java @@ -1,6 +1,7 @@ package org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode; import com.google.common.annotations.VisibleForTesting; +import com.google.common.collect.Sets; import htsjdk.samtools.SAMSequenceRecord; import htsjdk.samtools.reference.ReferenceSequence; import htsjdk.samtools.util.Locatable; @@ -23,7 +24,6 @@ import org.broadinstitute.hellbender.utils.param.ParamUtils; import org.broadinstitute.hellbender.utils.read.ReadUtils; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; -import org.testng.collections.Sets; import java.nio.file.Path; import java.util.*; @@ -108,16 +108,16 @@ public class GencodeFuncotationFactory extends DataSourceFuncotationFactory { */ private static final Set codingVariantClassifications = Sets.newHashSet(Arrays.asList(GencodeFuncotation.VariantClassification.MISSENSE, - GencodeFuncotation.VariantClassification.NONSENSE, - GencodeFuncotation.VariantClassification.NONSTOP, - GencodeFuncotation.VariantClassification.SILENT, - GencodeFuncotation.VariantClassification.IN_FRAME_DEL, - GencodeFuncotation.VariantClassification.IN_FRAME_INS, - GencodeFuncotation.VariantClassification.FRAME_SHIFT_INS, - GencodeFuncotation.VariantClassification.FRAME_SHIFT_DEL, - GencodeFuncotation.VariantClassification.START_CODON_SNP, - GencodeFuncotation.VariantClassification.START_CODON_INS, - GencodeFuncotation.VariantClassification.START_CODON_DEL)); + GencodeFuncotation.VariantClassification.NONSENSE, + GencodeFuncotation.VariantClassification.NONSTOP, + GencodeFuncotation.VariantClassification.SILENT, + GencodeFuncotation.VariantClassification.IN_FRAME_DEL, + GencodeFuncotation.VariantClassification.IN_FRAME_INS, + GencodeFuncotation.VariantClassification.FRAME_SHIFT_INS, + GencodeFuncotation.VariantClassification.FRAME_SHIFT_DEL, + GencodeFuncotation.VariantClassification.START_CODON_SNP, + GencodeFuncotation.VariantClassification.START_CODON_INS, + GencodeFuncotation.VariantClassification.START_CODON_DEL)); //================================================================================================================== diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java index 2aea9993260..652677957b0 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java @@ -2,14 +2,11 @@ import com.google.common.primitives.Ints; import htsjdk.variant.variantcontext.VariantContext; -import org.apache.commons.math.util.FastMath; +import org.apache.commons.math3.util.FastMath; import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.utils.MathUtils; -import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.help.HelpConstants; -import org.broadinstitute.hellbender.utils.read.AlignmentUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.read.ReadUtils; import java.util.List; import java.util.OptionalDouble; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadOrientationArtifact.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadOrientationArtifact.java index ba725473a20..bf3636601b8 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadOrientationArtifact.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadOrientationArtifact.java @@ -5,7 +5,7 @@ import htsjdk.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFFormatHeaderLine; -import org.apache.commons.math.util.FastMath; +import org.apache.commons.math3.util.FastMath; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.tools.walkers.readorientation.*; import org.broadinstitute.hellbender.utils.GATKProtectedVariantContextUtils; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java index 40aae82e6c0..31db5f6acdd 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java @@ -3,9 +3,12 @@ import htsjdk.samtools.SAMFileHeader; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.VariantContextWriter; -import htsjdk.variant.vcf.*; -import org.apache.commons.math.special.Beta; -import org.apache.commons.math.special.Gamma; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFStandardHeaderLines; +import org.apache.commons.math3.special.Beta; +import org.apache.commons.math3.special.Gamma; import org.apache.commons.math3.util.FastMath; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; @@ -21,7 +24,10 @@ import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler; import org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer; import org.broadinstitute.hellbender.transformers.ReadTransformer; -import org.broadinstitute.hellbender.utils.*; +import org.broadinstitute.hellbender.utils.MathUtils; +import org.broadinstitute.hellbender.utils.QualityUtils; +import org.broadinstitute.hellbender.utils.SimpleInterval; +import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState; import org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/python/StreamingPythonScriptExecutor.java b/src/main/java/org/broadinstitute/hellbender/utils/python/StreamingPythonScriptExecutor.java index f67b8332483..a491d517e33 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/python/StreamingPythonScriptExecutor.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/python/StreamingPythonScriptExecutor.java @@ -7,9 +7,11 @@ import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.runtime.*; -import org.testng.Assert; -import java.io.*; +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; import java.util.ArrayList; import java.util.List; import java.util.concurrent.Future; @@ -293,7 +295,9 @@ protected Process getProcess() { public void terminate() { if (dataTransferFIFOWriter != null) { if (asyncWriter != null) { - Assert.assertTrue(asyncWriter.terminate()); + if(!asyncWriter.terminate()){ + throw new GATKException("failed to close asyncWriter"); + } } spController.writeProcessInput(PYTHON_CLOSE_DATA_FIFO); sendAckRequest(); diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/testers/CleanSamTester.java b/src/main/java/org/broadinstitute/hellbender/utils/test/testers/CleanSamTester.java deleted file mode 100644 index f1ccbc299ca..00000000000 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/testers/CleanSamTester.java +++ /dev/null @@ -1,60 +0,0 @@ -package org.broadinstitute.hellbender.utils.test.testers; - -import htsjdk.samtools.*; -import htsjdk.samtools.util.CloserUtil; -import htsjdk.samtools.util.TestUtil; -import picard.sam.CleanSam; -import org.testng.Assert; - -import java.io.PrintWriter; -import java.util.*; - -/** - * This class is the extension of the SamFileTester to test CleanSam with SAM files generated on the fly. - */ -// TODO: this should live in the tests sources, because is testing just one class -// TODO: and it is not really part of the testing framework (which should be helpers for re-use with different classes) -public final class CleanSamTester extends SamFileTester { - private final String expectedCigar; - - @Override - public String getTestedToolName() { return CleanSam.class.getSimpleName(); } - - public CleanSamTester(final String expectedCigar, final int readLength, final int defaultChromosomeLength) { - super(readLength, true, defaultChromosomeLength); - this.expectedCigar = expectedCigar; - } - - - @Override - protected void test() { - try { - final SamFileValidator validator = new SamFileValidator(new PrintWriter(System.out), 8000); - - // Validate it has the expected cigar - validator.setIgnoreWarnings(true); - validator.setVerbose(true, 1000); - validator.setErrorsToIgnore(Collections.singletonList(SAMValidationError.Type.MISSING_READ_GROUP)); - SamReaderFactory factory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT); - SamReader samReader = factory.open(getOutput()); - final SAMRecordIterator iterator = samReader.iterator(); - while (iterator.hasNext()) { - final SAMRecord rec = iterator.next(); - Assert.assertEquals(rec.getCigarString(), expectedCigar); - if (SAMUtils.hasMateCigar(rec)) { - Assert.assertEquals(SAMUtils.getMateCigarString(rec), expectedCigar); - } - } - CloserUtil.close(samReader); - - // Run validation on the output file - samReader = factory.open(getOutput()); - final boolean validated = validator.validateSamFileVerbose(samReader, null); - CloserUtil.close(samReader); - - Assert.assertTrue(validated, "ValidateSamFile failed"); - } finally { - TestUtil.recursiveDelete(getOutputDir()); - } - } -} diff --git a/src/test/java/org/broadinstitute/hellbender/BwaMemIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/BwaMemIntegrationTest.java index 0d01c4178cd..d63e27b9d4a 100644 --- a/src/test/java/org/broadinstitute/hellbender/BwaMemIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/BwaMemIntegrationTest.java @@ -13,7 +13,7 @@ import org.broadinstitute.hellbender.utils.bwa.BwaMemAligner; import org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment; import org.broadinstitute.hellbender.utils.bwa.BwaMemIndex; -import org.broadinstitute.hellbender.utils.test.ReadTestUtils; +import org.broadinstitute.hellbender.testutils.ReadTestUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; diff --git a/src/test/java/org/broadinstitute/hellbender/CommandLineProgramTest.java b/src/test/java/org/broadinstitute/hellbender/CommandLineProgramTest.java index 1a4be742148..432f3df9e9b 100644 --- a/src/test/java/org/broadinstitute/hellbender/CommandLineProgramTest.java +++ b/src/test/java/org/broadinstitute/hellbender/CommandLineProgramTest.java @@ -1,13 +1,8 @@ package org.broadinstitute.hellbender; -import org.broadinstitute.hellbender.utils.runtime.ProcessController; -import org.broadinstitute.hellbender.utils.runtime.ProcessOutput; -import org.broadinstitute.hellbender.utils.runtime.ProcessSettings; -import org.broadinstitute.hellbender.utils.test.CommandLineProgramTester; -import org.testng.Assert; +import org.broadinstitute.hellbender.testutils.CommandLineProgramTester; import java.io.File; -import java.util.Arrays; import java.util.List; /** diff --git a/src/test/java/org/broadinstitute/hellbender/GATKBaseTest.java b/src/test/java/org/broadinstitute/hellbender/GATKBaseTest.java index 499bb9fccda..25751676902 100644 --- a/src/test/java/org/broadinstitute/hellbender/GATKBaseTest.java +++ b/src/test/java/org/broadinstitute/hellbender/GATKBaseTest.java @@ -5,7 +5,7 @@ import org.broadinstitute.hellbender.utils.GenomeLocParser; import org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.annotations.BeforeClass; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/IntelInflaterDeflaterIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/IntelInflaterDeflaterIntegrationTest.java index 41b653432c7..a3f44413d1f 100644 --- a/src/test/java/org/broadinstitute/hellbender/IntelInflaterDeflaterIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/IntelInflaterDeflaterIntegrationTest.java @@ -10,7 +10,7 @@ import htsjdk.samtools.util.zip.InflaterFactory; import org.broadinstitute.hellbender.utils.NativeUtils; import org.broadinstitute.hellbender.utils.RandomDNA; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.SkipException; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/cmdline/PicardCommandLineProgramExecutorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/cmdline/PicardCommandLineProgramExecutorIntegrationTest.java index b061056000c..548b9385e7d 100644 --- a/src/test/java/org/broadinstitute/hellbender/cmdline/PicardCommandLineProgramExecutorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/cmdline/PicardCommandLineProgramExecutorIntegrationTest.java @@ -2,7 +2,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.exceptions.PicardNonZeroExitException; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/CRAMSupportIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/CRAMSupportIntegrationTest.java index d2430f0e506..c452eb9df16 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/CRAMSupportIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/CRAMSupportIntegrationTest.java @@ -9,7 +9,7 @@ import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.tools.PrintReads; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/FeatureSupportIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/FeatureSupportIntegrationTest.java index 2b4318ff9d5..a24e13c5f6a 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/FeatureSupportIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/FeatureSupportIntegrationTest.java @@ -2,7 +2,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariants; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/GATKToolUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/GATKToolUnitTest.java index 4b90238c6fc..e1ad4181b2a 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/GATKToolUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/GATKToolUnitTest.java @@ -24,7 +24,7 @@ import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.reference.ReferenceUtils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/GatkToolIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/GatkToolIntegrationTest.java index 329bd066748..2e2a36224cb 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/GatkToolIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/GatkToolIntegrationTest.java @@ -6,7 +6,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/GenomicsDBIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/GenomicsDBIntegrationTest.java index f0f80af5164..0d370f8e438 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/GenomicsDBIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/GenomicsDBIntegrationTest.java @@ -5,10 +5,10 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.GenomicsDBTestUtils; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.GenomicsDBTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/PipelineSupportIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/PipelineSupportIntegrationTest.java index 22f406feb11..18055c98c4c 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/PipelineSupportIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/PipelineSupportIntegrationTest.java @@ -2,7 +2,7 @@ import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.runtime.ProcessController; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/ReadWalkerGCSSupportIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/ReadWalkerGCSSupportIntegrationTest.java index 0b9ae431cb7..5b933bd300e 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/ReadWalkerGCSSupportIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/ReadWalkerGCSSupportIntegrationTest.java @@ -4,8 +4,7 @@ import org.broadinstitute.hellbender.Main; import org.broadinstitute.hellbender.tools.PrintReads; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.testng.Assert; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/ReadWalkerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/ReadWalkerIntegrationTest.java index 49f3f500757..074a7e38b7e 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/ReadWalkerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/ReadWalkerIntegrationTest.java @@ -3,7 +3,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/ReadsDataSourceUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/ReadsDataSourceUnitTest.java index ebf3343d7a7..4fd5b024ae0 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/ReadsDataSourceUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/ReadsDataSourceUnitTest.java @@ -6,7 +6,7 @@ import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.XorWrapper; +import org.broadinstitute.hellbender.testutils.XorWrapper; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.ReadUtils; import org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/ReferenceMultiSourceUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/ReferenceMultiSourceUnitTest.java index f05f5e9f844..dfd5b50c678 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/ReferenceMultiSourceUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/ReferenceMultiSourceUnitTest.java @@ -4,7 +4,7 @@ import org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource; import org.broadinstitute.hellbender.engine.datasources.ReferenceWindowFunctions; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.SparkTestUtils; +import org.broadinstitute.hellbender.testutils.SparkTestUtils; import org.broadinstitute.hellbender.GATKBaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/ReferenceShardUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/ReferenceShardUnitTest.java index fbe754d00e1..332aab58787 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/ReferenceShardUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/ReferenceShardUnitTest.java @@ -2,7 +2,7 @@ import htsjdk.samtools.SAMRecord; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.ReadsPreprocessingPipelineTestData; +import org.broadinstitute.hellbender.testutils.ReadsPreprocessingPipelineTestData; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/VariantShardUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/VariantShardUnitTest.java index e2969ee77ea..1922ff463f3 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/VariantShardUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/VariantShardUnitTest.java @@ -3,7 +3,7 @@ import htsjdk.samtools.SAMRecord; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ReadsPreprocessingPipelineTestData; +import org.broadinstitute.hellbender.testutils.ReadsPreprocessingPipelineTestData; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/VariantWalkerGCSSupportIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/VariantWalkerGCSSupportIntegrationTest.java index 519ec0cb386..0a11c6e8bd8 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/VariantWalkerGCSSupportIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/VariantWalkerGCSSupportIntegrationTest.java @@ -4,7 +4,7 @@ import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/VariantWalkerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/VariantWalkerIntegrationTest.java index aefbd6c9e7b..0a491d84f49 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/VariantWalkerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/VariantWalkerIntegrationTest.java @@ -13,7 +13,7 @@ import org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker; import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/filters/ReadFilterLibraryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/filters/ReadFilterLibraryUnitTest.java index 9c7c5d1d04c..b78526e2442 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/filters/ReadFilterLibraryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/filters/ReadFilterLibraryUnitTest.java @@ -6,7 +6,7 @@ import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter; -import org.broadinstitute.hellbender.utils.test.ReadClipperTestUtils; +import org.broadinstitute.hellbender.testutils.ReadClipperTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSparkUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSparkUnitTest.java index 601271dbf4d..b5a43761ea0 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSparkUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSparkUnitTest.java @@ -17,15 +17,13 @@ import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.reference.ReferenceBases; -import org.broadinstitute.hellbender.utils.test.FakeReferenceSource; +import org.broadinstitute.hellbender.testutils.FakeReferenceSource; import org.broadinstitute.hellbender.utils.variant.GATKVariant; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import java.io.IOException; import java.io.Serializable; -import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.Map; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/DataprocIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/DataprocIntegrationTest.java index 7edf9ac56b4..de4310120de 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/DataprocIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/DataprocIntegrationTest.java @@ -2,7 +2,6 @@ import com.google.common.collect.Iterators; import htsjdk.samtools.ValidationStringency; -import htsjdk.samtools.util.Locatable; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.engine.ReadsDataSource; import org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark; @@ -12,9 +11,9 @@ import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.ReadCoordinateComparator; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.DataprocTestUtils; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.DataprocTestUtils; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; @@ -24,7 +23,6 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import java.nio.file.Paths; import java.util.Collections; import java.util.Iterator; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/JoinReadsWithRefBasesSparkUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/JoinReadsWithRefBasesSparkUnitTest.java index 9456fc422bd..04a55069565 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/JoinReadsWithRefBasesSparkUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/JoinReadsWithRefBasesSparkUnitTest.java @@ -11,13 +11,12 @@ import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.reference.ReferenceBases; -import org.broadinstitute.hellbender.utils.test.FakeReferenceSource; +import org.broadinstitute.hellbender.testutils.FakeReferenceSource; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.IOException; -import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.Map; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/ReadsPreprocessingPipelineSparkTestData.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/ReadsPreprocessingPipelineSparkTestData.java index 054488c4227..0b2c8631957 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/ReadsPreprocessingPipelineSparkTestData.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/ReadsPreprocessingPipelineSparkTestData.java @@ -11,7 +11,7 @@ import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.reference.ReferenceBases; -import org.broadinstitute.hellbender.utils.test.FakeReferenceSource; +import org.broadinstitute.hellbender.testutils.FakeReferenceSource; import org.broadinstitute.hellbender.utils.variant.GATKVariant; import org.broadinstitute.hellbender.utils.variant.MinimalVariant; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/SAMRecordSerializerUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/SAMRecordSerializerUnitTest.java index ea29f683da4..6303ab45799 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/SAMRecordSerializerUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/SAMRecordSerializerUnitTest.java @@ -6,7 +6,7 @@ import org.apache.spark.serializer.KryoRegistrator; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter; -import org.broadinstitute.hellbender.utils.test.SparkTestUtils; +import org.broadinstitute.hellbender.testutils.SparkTestUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/SAMRecordToGATKReadAdapterSerializerUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/SAMRecordToGATKReadAdapterSerializerUnitTest.java index 0099726c58b..7b0e5fde600 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/SAMRecordToGATKReadAdapterSerializerUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/SAMRecordToGATKReadAdapterSerializerUnitTest.java @@ -6,7 +6,7 @@ import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter; -import org.broadinstitute.hellbender.utils.test.SparkTestUtils; +import org.broadinstitute.hellbender.testutils.SparkTestUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSinkUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSinkUnitTest.java index 567e240dd13..d1a1c124e49 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSinkUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSinkUnitTest.java @@ -17,8 +17,7 @@ import org.broadinstitute.hellbender.utils.read.ReadCoordinateComparator; import org.broadinstitute.hellbender.utils.read.ReadsWriteFormat; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; -import org.broadinstitute.hellbender.utils.test.ReadTestUtils; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; import org.seqdoop.hadoop_bam.SplittingBAMIndexer; import org.testng.Assert; import org.testng.annotations.AfterClass; @@ -31,7 +30,6 @@ import java.nio.file.Files; import java.util.ArrayList; import java.util.Comparator; -import java.util.Iterator; import java.util.List; public class ReadsSparkSinkUnitTest extends GATKBaseTest { diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSourceUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSourceUnitTest.java index 7664e399a0e..74764047fac 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSourceUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSourceUnitTest.java @@ -7,30 +7,23 @@ import org.apache.hadoop.fs.Path; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FlatMapFunction; import org.broadinstitute.hellbender.engine.ReadsDataSource; import org.broadinstitute.hellbender.engine.TraversalParameters; import org.broadinstitute.hellbender.engine.spark.SparkContextFactory; -import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.ReadConstants; import org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.spark.SparkUtils; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.File; import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Iterator; import java.util.List; import static org.testng.Assert.assertEquals; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSinkUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSinkUnitTest.java index 85bc13e7e51..2256bade732 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSinkUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSinkUnitTest.java @@ -3,11 +3,9 @@ import com.google.common.io.Files; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; -import htsjdk.samtools.SamStreams; import htsjdk.samtools.seekablestream.SeekablePathStream; import htsjdk.samtools.seekablestream.SeekableStream; import htsjdk.samtools.util.BlockCompressedInputStream; -import htsjdk.tribble.AbstractFeatureReader; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.VariantContext; @@ -27,8 +25,8 @@ import org.broadinstitute.hellbender.utils.gcs.BucketUtils; import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.seqdoop.hadoop_bam.VCFFormat; import org.seqdoop.hadoop_bam.util.VCFHeaderReader; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSourceUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSourceUnitTest.java index 99ae6770af8..e012cb3e434 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSourceUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSourceUnitTest.java @@ -9,7 +9,7 @@ import org.broadinstitute.hellbender.engine.datasources.VariantsSource; import org.broadinstitute.hellbender.engine.spark.SparkContextFactory; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.variant.GATKVariant; import org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/metrics/MetricsUtilsTest.java b/src/test/java/org/broadinstitute/hellbender/metrics/MetricsUtilsTest.java index 10a356410ec..25f1cac02ea 100644 --- a/src/test/java/org/broadinstitute/hellbender/metrics/MetricsUtilsTest.java +++ b/src/test/java/org/broadinstitute/hellbender/metrics/MetricsUtilsTest.java @@ -5,7 +5,7 @@ import org.apache.hadoop.hdfs.MiniDFSCluster; import org.broadinstitute.hellbender.utils.gcs.BucketUtils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilderTest.java b/src/test/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilderTest.java similarity index 97% rename from src/test/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilderTest.java rename to src/test/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilderTest.java index 251e0e2ad38..0aed1e7edb8 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilderTest.java +++ b/src/test/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilderTest.java @@ -1,6 +1,7 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/ArtificialAnnotationUtils.java b/src/test/java/org/broadinstitute/hellbender/testutils/ArtificialAnnotationUtils.java similarity index 99% rename from src/test/java/org/broadinstitute/hellbender/utils/test/ArtificialAnnotationUtils.java rename to src/test/java/org/broadinstitute/hellbender/testutils/ArtificialAnnotationUtils.java index 1ce1bdf8b05..24f2f17844d 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/ArtificialAnnotationUtils.java +++ b/src/test/java/org/broadinstitute/hellbender/testutils/ArtificialAnnotationUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import com.google.common.collect.ImmutableMap; import htsjdk.samtools.TextCigarCodec; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/DataprocTestUtils.java b/src/test/java/org/broadinstitute/hellbender/testutils/DataprocTestUtils.java similarity index 98% rename from src/test/java/org/broadinstitute/hellbender/utils/test/DataprocTestUtils.java rename to src/test/java/org/broadinstitute/hellbender/testutils/DataprocTestUtils.java index c4f285bbe25..732534e6327 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/DataprocTestUtils.java +++ b/src/test/java/org/broadinstitute/hellbender/testutils/DataprocTestUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorReferenceTestUtils.java b/src/test/java/org/broadinstitute/hellbender/testutils/FuncotatorReferenceTestUtils.java similarity index 99% rename from src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorReferenceTestUtils.java rename to src/test/java/org/broadinstitute/hellbender/testutils/FuncotatorReferenceTestUtils.java index 7eaccca9785..3ad58665aae 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/FuncotatorReferenceTestUtils.java +++ b/src/test/java/org/broadinstitute/hellbender/testutils/FuncotatorReferenceTestUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import htsjdk.samtools.util.Lazy; import org.apache.commons.compress.archivers.ArchiveEntry; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/IntegrationTestSpecUnitTest.java b/src/test/java/org/broadinstitute/hellbender/testutils/IntegrationTestSpecUnitTest.java similarity index 96% rename from src/test/java/org/broadinstitute/hellbender/utils/test/IntegrationTestSpecUnitTest.java rename to src/test/java/org/broadinstitute/hellbender/testutils/IntegrationTestSpecUnitTest.java index 589be08dee5..750f3029f59 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/IntegrationTestSpecUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/testutils/IntegrationTestSpecUnitTest.java @@ -1,8 +1,9 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.exceptions.GATKException; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.broadinstitute.hellbender.tools.PrintReadsIntegrationTest; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/ReadTestUtils.java b/src/test/java/org/broadinstitute/hellbender/testutils/ReadTestUtils.java similarity index 99% rename from src/test/java/org/broadinstitute/hellbender/utils/test/ReadTestUtils.java rename to src/test/java/org/broadinstitute/hellbender/testutils/ReadTestUtils.java index 7b7e01a6736..95c024f6230 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/ReadTestUtils.java +++ b/src/test/java/org/broadinstitute/hellbender/testutils/ReadTestUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import htsjdk.samtools.*; import htsjdk.samtools.reference.IndexedFastaSequenceFile; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/SamAssertionUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/testutils/SamAssertionUtilsUnitTest.java similarity index 97% rename from src/test/java/org/broadinstitute/hellbender/utils/test/SamAssertionUtilsUnitTest.java rename to src/test/java/org/broadinstitute/hellbender/testutils/SamAssertionUtilsUnitTest.java index 828b512924a..acc48c9b053 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/SamAssertionUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/testutils/SamAssertionUtilsUnitTest.java @@ -1,7 +1,8 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import htsjdk.samtools.ValidationStringency; import org.broadinstitute.hellbender.GATKBaseTest; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/VariantContextTestUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtilsUnitTest.java similarity index 99% rename from src/test/java/org/broadinstitute/hellbender/utils/test/VariantContextTestUtilsUnitTest.java rename to src/test/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtilsUnitTest.java index 8b8f07828ef..413d17e8e33 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/VariantContextTestUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtilsUnitTest.java @@ -1,10 +1,11 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFHeader; import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.exceptions.UserException; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/testers/AbstractMarkDuplicatesTester.java b/src/test/java/org/broadinstitute/hellbender/testutils/testers/AbstractMarkDuplicatesTester.java similarity index 99% rename from src/test/java/org/broadinstitute/hellbender/utils/test/testers/AbstractMarkDuplicatesTester.java rename to src/test/java/org/broadinstitute/hellbender/testutils/testers/AbstractMarkDuplicatesTester.java index 81a8b67b4f1..788bd3d64f5 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/testers/AbstractMarkDuplicatesTester.java +++ b/src/test/java/org/broadinstitute/hellbender/testutils/testers/AbstractMarkDuplicatesTester.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test.testers; +package org.broadinstitute.hellbender.testutils.testers; import htsjdk.samtools.*; import htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/ClipReadsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/ClipReadsIntegrationTest.java index 83cda37512c..c9ba049556c 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/ClipReadsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/ClipReadsIntegrationTest.java @@ -3,7 +3,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.broadinstitute.hellbender.utils.text.XReadLines; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/CountBasesIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/CountBasesIntegrationTest.java index 4853a8265c4..bcc30149141 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/CountBasesIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/CountBasesIntegrationTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.hellbender.tools; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/CountReadsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/CountReadsIntegrationTest.java index 7659d131ebb..a20c7b22486 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/CountReadsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/CountReadsIntegrationTest.java @@ -2,9 +2,8 @@ import org.broadinstitute.barclay.argparser.CommandLineException; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/CountVariantsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/CountVariantsIntegrationTest.java index b0de22ccab0..ddef4d28bf2 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/CountVariantsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/CountVariantsIntegrationTest.java @@ -2,7 +2,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.tools.walkers.CountVariants; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/FixCallSetSampleOrderingIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/FixCallSetSampleOrderingIntegrationTest.java index 390f7de4f1d..65f57f6f3f1 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/FixCallSetSampleOrderingIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/FixCallSetSampleOrderingIntegrationTest.java @@ -14,7 +14,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/GatherVcfsCloudIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/GatherVcfsCloudIntegrationTest.java index 7f58fc54fd6..313658ac67d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/GatherVcfsCloudIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/GatherVcfsCloudIntegrationTest.java @@ -10,8 +10,8 @@ import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.engine.FeatureDataSource; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.text.XReadLines; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; import org.testng.Assert; @@ -23,7 +23,6 @@ import java.util.*; import java.util.function.Function; import java.util.stream.Collectors; -import java.util.stream.Stream; import java.util.stream.StreamSupport; public class GatherVcfsCloudIntegrationTest extends CommandLineProgramTest{ diff --git a/src/test/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSparkIntegrationTest.java index 8e8631314a3..c842b4c2a6c 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSparkIntegrationTest.java @@ -13,7 +13,7 @@ import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.SparkTestUtils; +import org.broadinstitute.hellbender.testutils.SparkTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java index 68c8a9e63c7..e41b12502f4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java @@ -13,9 +13,9 @@ import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/AnnotateIntervalsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/AnnotateIntervalsIntegrationTest.java index aa92d7c9e8e..83ca68c19ee 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/AnnotateIntervalsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/AnnotateIntervalsIntegrationTest.java @@ -13,7 +13,7 @@ import org.broadinstitute.hellbender.utils.IntervalMergingRule; import org.broadinstitute.hellbender.utils.IntervalSetRule; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CallCopyRatioSegmentsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CallCopyRatioSegmentsIntegrationTest.java index 75ffbf5ea84..1ebaa17da3d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CallCopyRatioSegmentsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CallCopyRatioSegmentsIntegrationTest.java @@ -3,7 +3,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.tools.copynumber.formats.collections.CalledCopyRatioSegmentCollection; import org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioSegmentCollection; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CollectReadCountsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CollectReadCountsIntegrationTest.java index b16a2111af3..1a4264289c5 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CollectReadCountsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CollectReadCountsIntegrationTest.java @@ -1,22 +1,17 @@ package org.broadinstitute.hellbender.tools.copynumber; -import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection; import org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection; import org.broadinstitute.hellbender.utils.IntervalMergingRule; import org.broadinstitute.hellbender.utils.IntervalSetRule; -import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; -import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.File; -import java.util.List; /** * Integration test for {@link CollectReadCounts}. diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CreateReadCountPanelOfNormalsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CreateReadCountPanelOfNormalsIntegrationTest.java index ba589ebc88c..c21853d65b0 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CreateReadCountPanelOfNormalsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/CreateReadCountPanelOfNormalsIntegrationTest.java @@ -21,7 +21,7 @@ import org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotationSet; import org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/DenoiseReadCountsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/DenoiseReadCountsIntegrationTest.java index 1c29376afa7..ff5f4641693 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/DenoiseReadCountsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/DenoiseReadCountsIntegrationTest.java @@ -4,7 +4,7 @@ import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument; import org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioCollection; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidyIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidyIntegrationTest.java index dc5e11e168d..286dcbd602b 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidyIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidyIntegrationTest.java @@ -4,7 +4,7 @@ import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.annotations.Test; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java index f01dc447525..aad53feebee 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java @@ -5,7 +5,7 @@ import org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection; import org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument; import org.broadinstitute.hellbender.utils.IntervalMergingRule; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.annotations.Test; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/ModelSegmentsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/ModelSegmentsIntegrationTest.java index 06fcacc6a3a..5214b5f4b56 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/ModelSegmentsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/ModelSegmentsIntegrationTest.java @@ -10,7 +10,7 @@ import org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioParameter; import org.broadinstitute.hellbender.tools.copynumber.models.MultidimensionalModellerUnitTest; import org.broadinstitute.hellbender.tools.copynumber.segmentation.MultidimensionalKernelSegmenterUnitTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/PostprocessGermlineCNVCallsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/PostprocessGermlineCNVCallsIntegrationTest.java index 799af4dac37..a18eacb8028 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/PostprocessGermlineCNVCallsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/PostprocessGermlineCNVCallsIntegrationTest.java @@ -2,8 +2,8 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/PreprocessIntervalsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/PreprocessIntervalsIntegrationTest.java index 329ae9597b5..77f2523d0cf 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/PreprocessIntervalsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/PreprocessIntervalsIntegrationTest.java @@ -7,7 +7,7 @@ import org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection; import org.broadinstitute.hellbender.utils.IntervalMergingRule; import org.broadinstitute.hellbender.utils.IntervalSetRule; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleAssemblyRegionWalkerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleAssemblyRegionWalkerIntegrationTest.java index e27b8e404b9..baed4fef7e8 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleAssemblyRegionWalkerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleAssemblyRegionWalkerIntegrationTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.util.Arrays; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleAssemblyRegionWalkerSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleAssemblyRegionWalkerSparkIntegrationTest.java index 3b5b52193ad..92ef2f08e31 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleAssemblyRegionWalkerSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleAssemblyRegionWalkerSparkIntegrationTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleCollectMultiMetricsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleCollectMultiMetricsIntegrationTest.java index 3bb8708108e..59d738bbc8b 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleCollectMultiMetricsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleCollectMultiMetricsIntegrationTest.java @@ -3,9 +3,9 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.metrics.MetricAccumulationLevel; import org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleCollectMultiMetricsSpark; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleCollectSingleMetricsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleCollectSingleMetricsIntegrationTest.java index 1e20cead1d8..43ebeab72f4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleCollectSingleMetricsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleCollectSingleMetricsIntegrationTest.java @@ -2,9 +2,9 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleCollectSingleMetricsSpark; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleFeatureWalkerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleFeatureWalkerIntegrationTest.java index 141b6f8e157..bbd989d6a3e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleFeatureWalkerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleFeatureWalkerIntegrationTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.IOException; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleIntervalWalkerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleIntervalWalkerIntegrationTest.java index 1bd8c1e4309..0760e0d5742 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleIntervalWalkerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleIntervalWalkerIntegrationTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.IOException; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleIntervalWalkerSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleIntervalWalkerSparkIntegrationTest.java index 02b6b74a759..aa394b903c4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleIntervalWalkerSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleIntervalWalkerSparkIntegrationTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleLocusWalkerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleLocusWalkerIntegrationTest.java index dcc552a9087..6a591082d04 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleLocusWalkerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleLocusWalkerIntegrationTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.IOException; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExamplePostTraversalPythonExecutorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExamplePostTraversalPythonExecutorIntegrationTest.java index 7d75acc5edf..599d2ff504f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExamplePostTraversalPythonExecutorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExamplePostTraversalPythonExecutorIntegrationTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.IOException; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReadWalkerWithReferenceIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReadWalkerWithReferenceIntegrationTest.java index c5e6bfbde1a..4934f36c4a0 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReadWalkerWithReferenceIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReadWalkerWithReferenceIntegrationTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.IOException; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReadWalkerWithReferenceSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReadWalkerWithReferenceSparkIntegrationTest.java index 369c8ee1211..5ad5652e857 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReadWalkerWithReferenceSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleReadWalkerWithReferenceSparkIntegrationTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleStreamingPythonExecutorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleStreamingPythonExecutorIntegrationTest.java index 646e7195e80..40327f71306 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleStreamingPythonExecutorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleStreamingPythonExecutorIntegrationTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleTwoPassVariantWalkerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleTwoPassVariantWalkerIntegrationTest.java index 719ca05be81..1a9d40fee23 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleTwoPassVariantWalkerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleTwoPassVariantWalkerIntegrationTest.java @@ -4,7 +4,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.engine.FeatureDataSource; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleVariantWalkerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleVariantWalkerIntegrationTest.java index fd51359a6f1..6cb9c0389b1 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleVariantWalkerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleVariantWalkerIntegrationTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.IOException; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleVariantWalkerSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleVariantWalkerSparkIntegrationTest.java index 3904fb0cc4c..24b600a40f1 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleVariantWalkerSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleVariantWalkerSparkIntegrationTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.hellbender.tools.examples; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotationMapUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotationMapUnitTest.java index 56e83262201..e7619ad701b 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotationMapUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotationMapUnitTest.java @@ -20,8 +20,8 @@ import org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfCodec; import org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfFeature; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.BaseTest; -import org.broadinstitute.hellbender.utils.test.FuncotatorReferenceTestUtils; +import org.broadinstitute.hellbender.testutils.BaseTest; +import org.broadinstitute.hellbender.testutils.FuncotatorReferenceTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java index 617b74d7dc7..d080090fb47 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java @@ -20,10 +20,10 @@ import org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer; import org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants; import org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.FuncotatorReferenceTestUtils; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.FuncotatorReferenceTestUtils; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorUnitTest.java index d8b74362fb9..5f2a4dc7b31 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorUnitTest.java @@ -1,7 +1,6 @@ package org.broadinstitute.hellbender.tools.funcotator; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.BaseTest; /** * Unit tests for the {@link org.broadinstitute.hellbender.tools.funcotator}. diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorUtilsUnitTest.java index 4b0738e2bf3..e0c65cc8275 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorUtilsUnitTest.java @@ -23,7 +23,7 @@ import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.utils.read.ReadUtils; -import org.broadinstitute.hellbender.utils.test.FuncotatorReferenceTestUtils; +import org.broadinstitute.hellbender.testutils.FuncotatorReferenceTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/cosmic/CosmicFuncotationFactoryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/cosmic/CosmicFuncotationFactoryUnitTest.java index 7e3f1dc364c..d509d2a2260 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/cosmic/CosmicFuncotationFactoryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/cosmic/CosmicFuncotationFactoryUnitTest.java @@ -14,7 +14,7 @@ import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.FuncotatorReferenceTestUtils; +import org.broadinstitute.hellbender.testutils.FuncotatorReferenceTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java index 86e02345f82..a1b95ffa2be 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactoryUnitTest.java @@ -23,7 +23,7 @@ import org.broadinstitute.hellbender.utils.codecs.gencode.*; import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.utils.reference.ReferenceBases; -import org.broadinstitute.hellbender.utils.test.FuncotatorReferenceTestUtils; +import org.broadinstitute.hellbender.testutils.FuncotatorReferenceTestUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/vcf/VcfFuncotationFactoryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/vcf/VcfFuncotationFactoryUnitTest.java index b0ab503c2e1..94ae66d3660 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/vcf/VcfFuncotationFactoryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/vcf/VcfFuncotationFactoryUnitTest.java @@ -20,8 +20,8 @@ import org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.FuncotatorReferenceTestUtils; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.FuncotatorReferenceTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/LocatableXsvFuncotationFactoryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/LocatableXsvFuncotationFactoryUnitTest.java index 24995ff111f..be099ab728b 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/LocatableXsvFuncotationFactoryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/LocatableXsvFuncotationFactoryUnitTest.java @@ -16,7 +16,7 @@ import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature; -import org.broadinstitute.hellbender.utils.test.FuncotatorReferenceTestUtils; +import org.broadinstitute.hellbender.testutils.FuncotatorReferenceTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/SimpleKeyXsvFuncotationFactoryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/SimpleKeyXsvFuncotationFactoryUnitTest.java index 42d16ba5402..f39885f9b4f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/SimpleKeyXsvFuncotationFactoryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/xsv/SimpleKeyXsvFuncotationFactoryUnitTest.java @@ -14,7 +14,7 @@ import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.FuncotatorReferenceTestUtils; +import org.broadinstitute.hellbender.testutils.FuncotatorReferenceTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRendererUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRendererUnitTest.java index 0e8d6f3d61b..e099cc8cb62 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRendererUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRendererUnitTest.java @@ -14,7 +14,7 @@ import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory; import org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/metadata/SamplePairExtractorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/metadata/SamplePairExtractorUnitTest.java index f44adfdfafa..f3ea51fff0a 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/metadata/SamplePairExtractorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/metadata/SamplePairExtractorUnitTest.java @@ -4,7 +4,7 @@ import htsjdk.variant.vcf.VCFHeader; import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java index 3cafb29e971..a8b8767bcb0 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java @@ -22,9 +22,9 @@ import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.gcs.BucketUtils; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.BaseTest; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.BaseTest; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/ApplyBQSRSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/ApplyBQSRSparkIntegrationTest.java index 6a92ce93f93..d650c51bc7a 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/ApplyBQSRSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/ApplyBQSRSparkIntegrationTest.java @@ -4,9 +4,9 @@ import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSparkIntegrationTest.java index 5b457f50db2..471c292631a 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSparkIntegrationTest.java @@ -6,10 +6,10 @@ import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.tools.walkers.bqsr.BQSRTestData; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSparkShardedIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSparkShardedIntegrationTest.java index ebb1ac86df8..7ba80923d91 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSparkShardedIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSparkShardedIntegrationTest.java @@ -6,9 +6,9 @@ import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.tools.walkers.bqsr.BQSRTestData; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/CreateHadoopBamSplittingIndexIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/CreateHadoopBamSplittingIndexIntegrationTest.java index 83493248668..ffae54f3e66 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/CreateHadoopBamSplittingIndexIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/CreateHadoopBamSplittingIndexIntegrationTest.java @@ -6,7 +6,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.seqdoop.hadoop_bam.SplittingBAMIndex; import org.seqdoop.hadoop_bam.SplittingBAMIndexer; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/ParallelCopyGCSDirectoryIntoHDFSSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/ParallelCopyGCSDirectoryIntoHDFSSparkIntegrationTest.java index b3d8500bed2..aef3b579ce8 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/ParallelCopyGCSDirectoryIntoHDFSSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/ParallelCopyGCSDirectoryIntoHDFSSparkIntegrationTest.java @@ -7,9 +7,9 @@ import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.gcs.BucketUtils; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java index 8ff78316550..126bf7e344e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java @@ -1,22 +1,15 @@ package org.broadinstitute.hellbender.tools.spark; import org.apache.hadoop.fs.Path; -import org.apache.hadoop.hdfs.MiniDFSCluster; -import org.apache.spark.api.java.JavaSparkContext; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.engine.spark.SparkContextFactory; -import org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource; -import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; -import org.testng.Assert; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.File; import java.io.IOException; -import java.util.List; /** * Integration tests for {@link PileupSpark}. diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaAndMarkDuplicatesPipelineSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaAndMarkDuplicatesPipelineSparkIntegrationTest.java index c9da134feb1..61364dc319d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaAndMarkDuplicatesPipelineSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaAndMarkDuplicatesPipelineSparkIntegrationTest.java @@ -3,8 +3,8 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection; import org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaSparkIntegrationTest.java index 7519c9bb2ea..6a391e62539 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/bwa/BwaSparkIntegrationTest.java @@ -3,8 +3,8 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.engine.spark.GATKSparkTool; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBuildKmersSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBuildKmersSparkIntegrationTest.java index 5470fb10dca..169f242184f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBuildKmersSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBuildKmersSparkIntegrationTest.java @@ -6,7 +6,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort; import org.broadinstitute.hellbender.tools.spark.utils.LongIterator; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBuildReferenceTaxonomyIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBuildReferenceTaxonomyIntegrationTest.java index 517fa9b7d05..59dffb9f610 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBuildReferenceTaxonomyIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBuildReferenceTaxonomyIntegrationTest.java @@ -3,7 +3,7 @@ import com.esotericsoftware.kryo.Kryo; import com.esotericsoftware.kryo.io.Input; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.BeforeTest; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBwaSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBwaSparkIntegrationTest.java index fd8a36d7127..4ae3d9ddc18 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBwaSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBwaSparkIntegrationTest.java @@ -2,8 +2,8 @@ import htsjdk.samtools.ValidationStringency; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqFilterSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqFilterSparkIntegrationTest.java index 8c3986335bf..a60799a1d45 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqFilterSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqFilterSparkIntegrationTest.java @@ -3,8 +3,8 @@ import htsjdk.samtools.ValidationStringency; import htsjdk.samtools.metrics.MetricsFile; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSparkIntegrationTest.java index 57016d39dea..36d464754c4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSparkIntegrationTest.java @@ -4,8 +4,8 @@ import htsjdk.samtools.metrics.MetricsFile; import org.apache.commons.io.FileUtils; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqScoreIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqScoreIntegrationTest.java index 6f6c4eafb34..fbaee94abee 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqScoreIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqScoreIntegrationTest.java @@ -3,7 +3,7 @@ import htsjdk.samtools.metrics.MetricsFile; import org.apache.commons.io.FileUtils; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/BQSRPipelineSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/BQSRPipelineSparkIntegrationTest.java index 24212c5125f..f282da15d21 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/BQSRPipelineSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/BQSRPipelineSparkIntegrationTest.java @@ -5,10 +5,10 @@ import org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSource; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.tools.walkers.bqsr.BQSRTestData; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountBasesSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountBasesSparkIntegrationTest.java index 882041a1ded..5cdb28c23af 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountBasesSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountBasesSparkIntegrationTest.java @@ -2,7 +2,7 @@ import org.apache.commons.io.FileUtils; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountReadsSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountReadsSparkIntegrationTest.java index 8782f1cddfa..79b6c76ae4f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountReadsSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountReadsSparkIntegrationTest.java @@ -3,7 +3,7 @@ import org.apache.commons.io.FileUtils; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.utils.text.XReadLines; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountVariantsSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountVariantsSparkIntegrationTest.java index 2700abe4b5f..2a4a1f455ee 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountVariantsSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountVariantsSparkIntegrationTest.java @@ -2,7 +2,7 @@ import org.apache.commons.io.FileUtils; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/FlagStatSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/FlagStatSparkIntegrationTest.java index 58ac6924ce7..4d1e1c7070a 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/FlagStatSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/FlagStatSparkIntegrationTest.java @@ -2,8 +2,8 @@ import com.google.common.collect.Lists; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/MarkDuplicatesSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/MarkDuplicatesSparkIntegrationTest.java index 64ec20aee15..dc0a996f0cb 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/MarkDuplicatesSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/MarkDuplicatesSparkIntegrationTest.java @@ -15,9 +15,9 @@ import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics; import org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesSparkTester; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.tools.walkers.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.testers.AbstractMarkDuplicatesTester; +import org.broadinstitute.hellbender.testutils.testers.AbstractMarkDuplicatesTester; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java index aaf3c598684..3754652b090 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java @@ -7,22 +7,18 @@ import java.io.File; import java.io.IOException; import java.util.Arrays; -import java.util.Collections; import java.util.Iterator; import java.util.List; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.engine.ReadsDataSource; -import org.broadinstitute.hellbender.engine.filters.ReadLengthReadFilter; -import org.broadinstitute.hellbender.engine.filters.ReadNameReadFilter; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.tools.PrintReadsIntegrationTest; import org.broadinstitute.hellbender.utils.gcs.BucketUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintVariantsSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintVariantsSparkIntegrationTest.java index 3f3cf002a76..f2d866b1917 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintVariantsSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintVariantsSparkIntegrationTest.java @@ -2,7 +2,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.utils.gcs.BucketUtils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSparkIntegrationTest.java index 3c752e8ed7c..339cb6f52c8 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSparkIntegrationTest.java @@ -5,9 +5,9 @@ import org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection; import org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSource; import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerIntegrationTest; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/SortSamSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/SortSamSparkIntegrationTest.java index 5ba8c7505f7..f2fb73b6ce4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/SortSamSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/SortSamSparkIntegrationTest.java @@ -11,12 +11,11 @@ import org.broadinstitute.hellbender.engine.spark.GATKSparkTool; import org.broadinstitute.hellbender.engine.spark.SparkContextFactory; import org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource; -import org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSpark; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.BaseTest; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.BaseTest; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectBaseDistributionByCycleSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectBaseDistributionByCycleSparkIntegrationTest.java index 87f316cb0c7..c4edfc8818e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectBaseDistributionByCycleSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectBaseDistributionByCycleSparkIntegrationTest.java @@ -1,9 +1,9 @@ package org.broadinstitute.hellbender.tools.spark.pipelines.metrics; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectInsertSizeMetricsSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectInsertSizeMetricsSparkIntegrationTest.java index 3f6ed6a4715..ed65539b65c 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectInsertSizeMetricsSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectInsertSizeMetricsSparkIntegrationTest.java @@ -4,9 +4,9 @@ import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary; import org.broadinstitute.hellbender.metrics.MetricAccumulationLevel; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectMultipleMetricsSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectMultipleMetricsSparkIntegrationTest.java index 8c493066228..a3078467ef7 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectMultipleMetricsSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectMultipleMetricsSparkIntegrationTest.java @@ -9,10 +9,10 @@ import org.broadinstitute.hellbender.metrics.MetricsArgumentCollection; import org.broadinstitute.hellbender.metrics.QualityYieldMetrics; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.metrics.InsertSizeMetrics; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectQualityYieldMetricsSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectQualityYieldMetricsSparkIntegrationTest.java index eb39b0c8741..30bf510745e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectQualityYieldMetricsSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/CollectQualityYieldMetricsSparkIntegrationTest.java @@ -1,9 +1,9 @@ package org.broadinstitute.hellbender.tools.spark.pipelines.metrics; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/InsertSizeMetricsCollectorSparkUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/InsertSizeMetricsCollectorSparkUnitTest.java index 2e25a99e027..63fa9dd77e0 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/InsertSizeMetricsCollectorSparkUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/InsertSizeMetricsCollectorSparkUnitTest.java @@ -13,7 +13,7 @@ import org.broadinstitute.hellbender.metrics.MetricAccumulationLevel; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/MeanQualityByCycleSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/MeanQualityByCycleSparkIntegrationTest.java index 2eaf238513c..7946349b4f9 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/MeanQualityByCycleSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/MeanQualityByCycleSparkIntegrationTest.java @@ -3,9 +3,9 @@ import htsjdk.samtools.metrics.MetricsFile; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/QualityScoreDistributionSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/QualityScoreDistributionSparkIntegrationTest.java index b803e08ac74..c5108c20e84 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/QualityScoreDistributionSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/QualityScoreDistributionSparkIntegrationTest.java @@ -7,9 +7,9 @@ import org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSpark.Counts; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/AnnotatedVariantProducerUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/AnnotatedVariantProducerUnitTest.java index e906d3ef859..17b27ba7bd9 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/AnnotatedVariantProducerUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/AnnotatedVariantProducerUnitTest.java @@ -27,7 +27,7 @@ import org.broadinstitute.hellbender.tools.spark.sv.utils.SVIntervalTree; import org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.mockito.Mockito; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SvDiscoveryUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SvDiscoveryUtilsUnitTest.java index 4c5da7b859f..c0e701839e8 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SvDiscoveryUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SvDiscoveryUtilsUnitTest.java @@ -7,7 +7,7 @@ import org.broadinstitute.hellbender.engine.spark.SparkContextFactory; import org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantCanonicalRepresentationUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantCanonicalRepresentationUnitTest.java index d583b8503fd..9dc8fcd6286 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantCanonicalRepresentationUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantCanonicalRepresentationUnitTest.java @@ -15,7 +15,7 @@ import org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments; import org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreterUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreterUnitTest.java index 2aadc461e59..6fc837e52a4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreterUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/CpxVariantInterpreterUnitTest.java @@ -12,7 +12,7 @@ import org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier; import org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.BeforeTest; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/ImpreciseVariantDetectorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/ImpreciseVariantDetectorUnitTest.java index c3486a61a69..d9cc948814b 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/ImpreciseVariantDetectorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/ImpreciseVariantDetectorUnitTest.java @@ -16,7 +16,7 @@ import org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree; import org.broadinstitute.hellbender.tools.spark.sv.utils.SVInterval; import org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.mockito.Mockito; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractorUnitTest.java index ac915c3dad6..05bc30d2853 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SegmentedCpxVariantSimpleVariantExtractorUnitTest.java @@ -12,7 +12,7 @@ import org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFWriter; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ReadMetadataTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ReadMetadataTest.java index ed12d82c8d4..10132f17fae 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ReadMetadataTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ReadMetadataTest.java @@ -7,7 +7,7 @@ import org.broadinstitute.hellbender.utils.IntHistogramTest; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/CpxVariantReInterpreterSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/CpxVariantReInterpreterSparkIntegrationTest.java index 56f69df1a96..dfe11a18968 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/CpxVariantReInterpreterSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/CpxVariantReInterpreterSparkIntegrationTest.java @@ -7,9 +7,9 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest.java index b0f1d4b6a86..bd2e67c9be0 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest.java @@ -3,9 +3,9 @@ import org.apache.hadoop.fs.Path; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/ExtractOriginalAlignmentRecordsByNameSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/ExtractOriginalAlignmentRecordsByNameSparkIntegrationTest.java index 17584776ed0..03a2f3c6731 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/ExtractOriginalAlignmentRecordsByNameSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/ExtractOriginalAlignmentRecordsByNameSparkIntegrationTest.java @@ -8,7 +8,7 @@ import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/FindBreakpointEvidenceSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/FindBreakpointEvidenceSparkIntegrationTest.java index ab776f80117..eb9ec78b19d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/FindBreakpointEvidenceSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/FindBreakpointEvidenceSparkIntegrationTest.java @@ -4,10 +4,10 @@ import org.apache.hadoop.hdfs.MiniDFSCluster; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.BaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.BaseTest; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java index e8891d7cb75..ff1f5630e68 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java @@ -9,10 +9,10 @@ import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.gcs.BucketUtils; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.BaseTest; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.BaseTest; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/SingleContigReferenceAlignerUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/SingleContigReferenceAlignerUnitTest.java index fbd20d012d0..acc5defd115 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/SingleContigReferenceAlignerUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/SingleContigReferenceAlignerUnitTest.java @@ -5,13 +5,12 @@ import htsjdk.samtools.CigarOperator; import htsjdk.samtools.TextCigarCodec; import htsjdk.samtools.util.SequenceUtil; -import org.apache.commons.math3.util.Pair; import org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig; import org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval; import org.broadinstitute.hellbender.utils.RandomDNA; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.read.CigarUtils; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSparkUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSparkUtilsUnitTest.java index fcb8058d3a8..f4acccfbd8f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSparkUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSparkUtilsUnitTest.java @@ -8,6 +8,7 @@ import org.broadinstitute.hellbender.engine.spark.SparkContextFactory; import org.broadinstitute.hellbender.utils.read.*; import org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy; + import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.read.markduplicates.SerializableOpticalDuplicatesFinder; import org.testng.Assert; @@ -15,6 +16,7 @@ import scala.Tuple2; import java.io.IOException; + import java.util.*; public class MarkDuplicatesSparkUtilsUnitTest extends GATKBaseTest { diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/validation/CompareDuplicatesSparkIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/validation/CompareDuplicatesSparkIntegrationTest.java index 6b8e46c820e..098ab68b8e1 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/spark/validation/CompareDuplicatesSparkIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/spark/validation/CompareDuplicatesSparkIntegrationTest.java @@ -8,9 +8,9 @@ import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.ReadQueryNameComparator; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.ReadTestUtils; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ReadTestUtils; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/validation/CompareBaseQualitiesIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/validation/CompareBaseQualitiesIntegrationTest.java index f07d180b7b3..1123ca2aabf 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/validation/CompareBaseQualitiesIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/validation/CompareBaseQualitiesIntegrationTest.java @@ -1,9 +1,9 @@ package org.broadinstitute.hellbender.tools.validation; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java index 007bf0dfe8e..ba4e3a7709f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java @@ -1,9 +1,6 @@ package org.broadinstitute.hellbender.tools.walkers; import htsjdk.samtools.seekablestream.SeekablePathStream; -import htsjdk.tribble.readers.LineIterator; -import htsjdk.tribble.readers.PositionalBufferedStream; -import htsjdk.variant.vcf.VCFCodec; import htsjdk.variant.vcf.VCFHeader; import org.apache.commons.codec.digest.DigestUtils; import htsjdk.variant.variantcontext.VariantContext; @@ -11,24 +8,18 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.engine.FeatureDataSource; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.utils.runtime.ProcessController; import org.broadinstitute.hellbender.utils.runtime.ProcessOutput; import org.broadinstitute.hellbender.utils.runtime.ProcessSettings; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.seqdoop.hadoop_bam.util.VCFHeaderReader; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.File; -import java.io.FileInputStream; import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.nio.file.StandardCopyOption; import java.security.NoSuchAlgorithmException; import java.util.ArrayList; import java.util.Arrays; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java index e5b67a979c2..d44ad416df5 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java @@ -3,10 +3,7 @@ import htsjdk.samtools.seekablestream.SeekablePathStream; import htsjdk.samtools.util.Locatable; import htsjdk.tribble.Tribble; -import htsjdk.tribble.readers.LineIterator; -import htsjdk.tribble.readers.PositionalBufferedStream; import htsjdk.variant.variantcontext.VariantContext; -import htsjdk.variant.vcf.VCFCodec; import htsjdk.variant.vcf.VCFHeader; import org.apache.commons.codec.digest.DigestUtils; import org.apache.commons.collections.IteratorUtils; @@ -18,16 +15,15 @@ import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.utils.runtime.ProcessController; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.GenomicsDBTestUtils; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.GenomicsDBTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.seqdoop.hadoop_bam.util.VCFHeaderReader; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.File; -import java.io.FileInputStream; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsUnitTest.java index efc2ec673bb..1da63e6b4e5 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsUnitTest.java @@ -2,7 +2,7 @@ import htsjdk.variant.variantcontext.*; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMergerUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMergerUnitTest.java index 4b4ce5781cb..e7b92a99763 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMergerUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMergerUnitTest.java @@ -8,7 +8,7 @@ import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/UnmarkDuplicatesIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/UnmarkDuplicatesIntegrationTest.java index bde336a4b3d..7aca92a0fb3 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/UnmarkDuplicatesIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/UnmarkDuplicatesIntegrationTest.java @@ -5,7 +5,7 @@ import htsjdk.samtools.SamReader; import htsjdk.samtools.SamReaderFactory; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/ValidateVariantsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/ValidateVariantsIntegrationTest.java index 2a796678c48..ded49ab640d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/ValidateVariantsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/ValidateVariantsIntegrationTest.java @@ -1,9 +1,8 @@ package org.broadinstitute.hellbender.tools.walkers; -import htsjdk.tribble.TribbleException; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTestUnitTest.java index 53200e32b39..47fe0bb6f4d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQualityRankSumTestUnitTest.java @@ -7,7 +7,7 @@ import org.broadinstitute.hellbender.utils.genotyper.*; import org.broadinstitute.hellbender.utils.genotyper.SampleList; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ClippingRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ClippingRankSumTestUnitTest.java index dd0aedd0198..f4ac0c2b3ff 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ClippingRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ClippingRankSumTestUnitTest.java @@ -8,7 +8,7 @@ import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/CoverageUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/CoverageUnitTest.java index c9975c03ada..c26146b2b6d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/CoverageUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/CoverageUnitTest.java @@ -14,7 +14,7 @@ import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.GATKBaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySampleUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySampleUnitTest.java index 28a2af5f114..0483132ef8e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySampleUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySampleUnitTest.java @@ -1,7 +1,6 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; import com.google.common.collect.ImmutableMap; -import com.google.common.collect.Lists; import htsjdk.samtools.TextCigarCodec; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.VCFConstants; @@ -9,7 +8,7 @@ import org.broadinstitute.hellbender.utils.genotyper.*; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.GATKBaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerSampleHCUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerSampleHCUnitTest.java index c36bd8bd1c2..ec736fb2150 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerSampleHCUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerSampleHCUnitTest.java @@ -4,7 +4,7 @@ import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.GATKBaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrandUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrandUnitTest.java index 1f9c36b6ac6..8831d6a5d8d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrandUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/FisherStrandUnitTest.java @@ -9,7 +9,7 @@ import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTestUnitTest.java index 73ccbb18ce1..7d687d25ff2 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/LikelihoodRankSumTestUnitTest.java @@ -8,7 +8,7 @@ import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityRankSumTestUnitTest.java index 98dd33a3cd4..7ca2f7a9c90 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityRankSumTestUnitTest.java @@ -7,7 +7,7 @@ import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityZeroUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityZeroUnitTest.java index 7a9704516f6..6e821153d60 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityZeroUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQualityZeroUnitTest.java @@ -12,7 +12,7 @@ import org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/OxoGReadCountsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/OxoGReadCountsUnitTest.java index c5a95da557d..877d9287519 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/OxoGReadCountsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/OxoGReadCountsUnitTest.java @@ -10,7 +10,7 @@ import org.broadinstitute.hellbender.utils.genotyper.*; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.utils.read.ReadUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepthUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepthUnitTest.java index 3a4458dfefa..99f0cfbcd39 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepthUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepthUnitTest.java @@ -8,7 +8,7 @@ import org.broadinstitute.hellbender.utils.genotyper.*; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java index f97113581d2..6494c915edd 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQualityUnitTest.java @@ -16,7 +16,7 @@ import org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTestUnitTest.java index ca74dde0536..78ceae09fc3 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosRankSumTestUnitTest.java @@ -11,7 +11,7 @@ import org.broadinstitute.hellbender.utils.genotyper.*; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatioUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatioUnitTest.java index 82fe2089f40..665946751e2 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatioUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandOddsRatioUnitTest.java @@ -8,7 +8,7 @@ import org.broadinstitute.hellbender.utils.genotyper.*; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngineUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngineUnitTest.java index 6d58c7e95a7..03025c79507 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngineUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngineUnitTest.java @@ -15,9 +15,9 @@ import org.broadinstitute.hellbender.utils.genotyper.*; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java index c67945c11a2..2e226473019 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -9,10 +9,9 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.engine.FeatureDataSource; -import org.broadinstitute.hellbender.engine.FeatureDataSourceUnitTest; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.seqdoop.hadoop_bam.util.VCFHeaderReader; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTestUnitTest.java index 46c4603edc6..309e5273868 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_BaseQualityRankSumTestUnitTest.java @@ -1,10 +1,9 @@ package org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific; -import com.google.common.primitives.Doubles; import htsjdk.variant.variantcontext.*; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.tools.walkers.annotator.Annotation; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityRankSumTestUnitTest; import org.broadinstitute.hellbender.utils.MannWhitneyU; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTestUnitTest.java index cc3814e9564..80290038602 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_MappingQualityRankSumTestUnitTest.java @@ -5,7 +5,7 @@ import htsjdk.variant.variantcontext.*; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.tools.walkers.annotator.Annotation; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.utils.MannWhitneyU; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTestUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTestUnitTest.java index 7af862f1b98..0dc7ce4c1c7 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTestUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_ReadPosRankSumTestUnitTest.java @@ -5,7 +5,7 @@ import htsjdk.variant.variantcontext.*; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.tools.walkers.annotator.Annotation; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.utils.MannWhitneyU; import org.broadinstitute.hellbender.utils.QualityUtils; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java index abf7f163549..073f9a8ab49 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotationBaseTest.java @@ -12,7 +12,7 @@ import org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.GeneralPloidyFailOverAFCalculatorProvider; import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java index 20c831970b4..3b6f165d3c4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java @@ -3,7 +3,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.broadinstitute.hellbender.utils.Utils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/ApplyBQSRIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/ApplyBQSRIntegrationTest.java index a81ebdd77be..9c5c878a886 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/ApplyBQSRIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/ApplyBQSRIntegrationTest.java @@ -4,7 +4,6 @@ import com.google.common.jimfs.Jimfs; import htsjdk.samtools.SamReaderFactory; import java.nio.file.FileSystem; -import java.nio.file.Files; import java.nio.file.Path; import org.apache.commons.lang.StringUtils; import org.broadinstitute.barclay.argparser.CommandLineException; @@ -13,8 +12,8 @@ import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.gcs.BucketUtils; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibratorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibratorIntegrationTest.java index 99a98260450..40f5a7019e6 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibratorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibratorIntegrationTest.java @@ -6,8 +6,8 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.broadinstitute.hellbender.utils.Utils; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BothStepsOfBQSRIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BothStepsOfBQSRIntegrationTest.java index c9bd448a8b5..b2f6ce6d54f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BothStepsOfBQSRIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BothStepsOfBQSRIntegrationTest.java @@ -4,7 +4,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.Main; import org.broadinstitute.hellbender.tools.validation.CompareBaseQualities; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/GatherBQSRReportsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/GatherBQSRReportsIntegrationTest.java index eb3a6d06dbd..00938e3c04a 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/GatherBQSRReportsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/GatherBQSRReportsIntegrationTest.java @@ -2,9 +2,9 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltrationIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltrationIntegrationTest.java index cc9fd5dc95f..ed0a5360cc9 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltrationIntegrationTest.java @@ -3,7 +3,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtilsUnitTest.java index f28083243aa..53fde23c6df 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtilsUnitTest.java @@ -4,7 +4,7 @@ import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.hellbender.utils.MathUtils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 70b60196ccc..d4c0b91eec2 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -8,7 +8,6 @@ import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFHeader; -import java.nio.file.Path; import org.apache.commons.collections.CollectionUtils; import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.barclay.argparser.CommandLineException; @@ -17,6 +16,9 @@ import org.broadinstitute.hellbender.engine.FeatureDataSource; import org.broadinstitute.hellbender.engine.ReadsDataSource; import org.broadinstitute.hellbender.exceptions.UserException; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils; import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection; import org.broadinstitute.hellbender.utils.SimpleInterval; @@ -24,9 +26,6 @@ import org.broadinstitute.hellbender.utils.gcs.BucketUtils; import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants; import org.testng.Assert; @@ -35,6 +34,7 @@ import java.io.File; import java.io.IOException; +import java.nio.file.Path; import java.util.*; import java.util.stream.Collectors; import java.util.stream.StreamSupport; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/AbstractMarkDuplicatesCommandLineProgramTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/AbstractMarkDuplicatesCommandLineProgramTest.java index 10911331d8e..29adf54a717 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/AbstractMarkDuplicatesCommandLineProgramTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/AbstractMarkDuplicatesCommandLineProgramTest.java @@ -7,14 +7,11 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.CommandLineProgram; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; -import org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection; -import org.broadinstitute.hellbender.tools.spark.pipelines.MarkDuplicatesSparkIntegrationTest; -import org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.BaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; -import org.broadinstitute.hellbender.utils.test.testers.AbstractMarkDuplicatesTester; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.BaseTest; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.testers.AbstractMarkDuplicatesTester; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/MarkDuplicatesGATKIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/MarkDuplicatesGATKIntegrationTest.java index 39b57cb927d..2d591ba2f65 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/MarkDuplicatesGATKIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/MarkDuplicatesGATKIntegrationTest.java @@ -8,8 +8,8 @@ import org.broadinstitute.hellbender.cmdline.CommandLineProgram; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesTester; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.testers.AbstractMarkDuplicatesTester; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.testers.AbstractMarkDuplicatesTester; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/CreateSomaticPanelOfNormalsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/CreateSomaticPanelOfNormalsIntegrationTest.java index d8ea0bf005b..afd05bb2f0b 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/CreateSomaticPanelOfNormalsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/CreateSomaticPanelOfNormalsIntegrationTest.java @@ -3,7 +3,7 @@ import htsjdk.variant.variantcontext.VariantContext; import org.apache.commons.io.FileUtils; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/FilteringFirstPassUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/FilteringFirstPassUnitTest.java index b688a988a85..2714364c8f9 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/FilteringFirstPassUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/FilteringFirstPassUnitTest.java @@ -1,14 +1,11 @@ package org.broadinstitute.hellbender.tools.walkers.mutect; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.GATKBaseTest; import org.testng.Assert; -import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import java.util.Optional; - -public class FilteringFirstPassUnitTest extends BaseTest { +public class FilteringFirstPassUnitTest extends GATKBaseTest { @DataProvider(name = "falsePositiveRateData") public Object[][] makeFalsePositiveRateData() { return new Object[][]{ diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java index 08576deed9d..4b283d3a49d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java @@ -16,8 +16,8 @@ import org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord; import org.broadinstitute.hellbender.utils.MathUtils; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/StrandArtifactUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/StrandArtifactUnitTest.java index c5723e6030b..e465529df2e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/StrandArtifactUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/StrandArtifactUnitTest.java @@ -10,7 +10,7 @@ import org.broadinstitute.hellbender.utils.genotyper.*; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.test.ArtificialAnnotationUtils; +import org.broadinstitute.hellbender.testutils.ArtificialAnnotationUtils; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/qc/CheckPileupIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/qc/CheckPileupIntegrationTest.java index fd76ab66b5d..b63589ae54d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/qc/CheckPileupIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/qc/CheckPileupIntegrationTest.java @@ -1,8 +1,7 @@ package org.broadinstitute.hellbender.tools.walkers.qc; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/qc/PileupIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/qc/PileupIntegrationTest.java index 300c0a36e13..734f7df0ac4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/qc/PileupIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/qc/PileupIntegrationTest.java @@ -2,13 +2,11 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.IOException; -import java.util.ArrayList; import java.util.Arrays; -import java.util.List; /** * @author Daniel Gomez-Sanchez (magicDGS) diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/readorientation/AltSiteRecordUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/readorientation/AltSiteRecordUnitTest.java index 61a1ec0f008..27e1793dc66 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/readorientation/AltSiteRecordUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/readorientation/AltSiteRecordUnitTest.java @@ -1,7 +1,8 @@ package org.broadinstitute.hellbender.tools.walkers.readorientation; +import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.Nucleotide; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; @@ -15,7 +16,7 @@ /** * Created by tsato on 10/16/17. */ -public class AltSiteRecordUnitTest extends BaseTest { +public class AltSiteRecordUnitTest extends GATKBaseTest { @Test public void test() throws IOException { File table = BaseTest.createTempFile("alt-site-design-matrix","tsv"); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java index 25d208179b7..0fa8c009f61 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java @@ -1,13 +1,12 @@ package org.broadinstitute.hellbender.tools.walkers.rnaseq; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.broadinstitute.hellbender.exceptions.UserException; import org.testng.annotations.Test; -import java.io.File; import java.util.Arrays; public final class ASEReadCounterIntegrationTest extends CommandLineProgramTest { diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java index fa5aebc066c..00d0be0c5ef 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.hellbender.tools.walkers.rnaseq; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java index b0a7c38f29b..a75d63699b7 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java @@ -8,7 +8,7 @@ import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.GATKReadWriter; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.ReadClipperTestUtils; +import org.broadinstitute.hellbender.testutils.ReadClipperTestUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithBamDepthIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithBamDepthIntegrationTest.java index 5c2ed1a44fe..736cf8eb67e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithBamDepthIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithBamDepthIntegrationTest.java @@ -3,7 +3,7 @@ import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithExpectedAlleleFractionIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithExpectedAlleleFractionIntegrationTest.java index 0056fccda6d..28ab713a78f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithExpectedAlleleFractionIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithExpectedAlleleFractionIntegrationTest.java @@ -3,7 +3,7 @@ import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/ConcordanceIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/ConcordanceIntegrationTest.java index c203767ebc3..223a98c02b3 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/ConcordanceIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/ConcordanceIntegrationTest.java @@ -3,7 +3,7 @@ import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.engine.AbstractConcordanceWalker; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/RemoveNearbyIndelsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/RemoveNearbyIndelsIntegrationTest.java index 10b4bbaba7e..d57fce93bd0 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/RemoveNearbyIndelsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/RemoveNearbyIndelsIntegrationTest.java @@ -3,7 +3,7 @@ import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java index 069df4a128f..25420825ecd 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java @@ -4,8 +4,8 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariantsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariantsIntegrationTest.java index 70a0517f4d6..ec670f09126 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -8,7 +8,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import java.io.File; import java.io.IOException; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/UpdateVCFSequenceDictionaryIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/UpdateVCFSequenceDictionaryIntegrationTest.java index 7d05c30cdbc..8f13793f628 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/UpdateVCFSequenceDictionaryIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/UpdateVCFSequenceDictionaryIntegrationTest.java @@ -6,7 +6,7 @@ import htsjdk.variant.vcf.VCFHeader; import org.broadinstitute.barclay.argparser.CommandLineException; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java index f82c956f0b6..e8d43fb9f98 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java @@ -2,7 +2,7 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.IOException; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/ApplyVQSRIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/ApplyVQSRIntegrationTest.java index 2eadfa229c1..745ab7ad030 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/ApplyVQSRIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/ApplyVQSRIntegrationTest.java @@ -9,8 +9,8 @@ import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.engine.FeatureDataSource; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariantsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariantsIntegrationTest.java index 6ce7ba8df21..42344dd713d 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariantsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariantsIntegrationTest.java @@ -2,8 +2,8 @@ import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.IOException; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantPipelineTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantPipelineTest.java index 12dce833fd7..899174328a4 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantPipelineTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantPipelineTest.java @@ -2,7 +2,7 @@ import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.Main; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/FilterVariantTranchesIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/FilterVariantTranchesIntegrationTest.java index 93d12a36e38..3dbe6aee609 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/FilterVariantTranchesIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/FilterVariantTranchesIntegrationTest.java @@ -1,8 +1,8 @@ package org.broadinstitute.hellbender.tools.walkers.vqsr; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranchesIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranchesIntegrationTest.java index 4019923c5cd..2c503b2f9a5 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranchesIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranchesIntegrationTest.java @@ -1,9 +1,9 @@ package org.broadinstitute.hellbender.tools.walkers.vqsr; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibratorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibratorIntegrationTest.java index 4a56bcd4c9b..d33aed2a286 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibratorIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibratorIntegrationTest.java @@ -1,10 +1,9 @@ package org.broadinstitute.hellbender.tools.walkers.vqsr; -import org.apache.commons.lang.StringUtils; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/R/RScriptExecutorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/R/RScriptExecutorUnitTest.java index c790a524ec2..ef7a7bac947 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/R/RScriptExecutorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/R/RScriptExecutorUnitTest.java @@ -3,7 +3,7 @@ import org.apache.commons.io.FileUtils; import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/R/RScriptLibraryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/R/RScriptLibraryUnitTest.java index 5175e5b82c7..0d92ca9f21f 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/R/RScriptLibraryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/R/RScriptLibraryUnitTest.java @@ -1,6 +1,6 @@ package org.broadinstitute.hellbender.utils.R; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/clipping/ReadClipperUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/clipping/ReadClipperUnitTest.java index cd921be8311..da35d1fbb49 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/clipping/ReadClipperUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/clipping/ReadClipperUnitTest.java @@ -5,7 +5,7 @@ import org.broadinstitute.hellbender.utils.read.CigarUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.ReadClipperTestUtils; +import org.broadinstitute.hellbender.testutils.ReadClipperTestUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigIntegrationTest.java index a11e69c8efc..eaf1083e119 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigIntegrationTest.java @@ -7,7 +7,7 @@ import org.broadinstitute.hellbender.cmdline.TestProgramGroup; import org.broadinstitute.hellbender.engine.GATKTool; import org.broadinstitute.hellbender.exceptions.GATKException; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigPrintReadsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigPrintReadsIntegrationTest.java index e04bbf11096..32553be0d9b 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigPrintReadsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigPrintReadsIntegrationTest.java @@ -5,8 +5,8 @@ import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.tools.PrintReads; -import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.testng.annotations.Test; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigUnitTest.java index 7b80e21d50a..f38e7d4f043 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/config/ConfigUnitTest.java @@ -6,7 +6,7 @@ import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.exceptions.UserException; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/gcs/BucketUtilsTest.java b/src/test/java/org/broadinstitute/hellbender/utils/gcs/BucketUtilsTest.java index 83bf6d25a75..092c4a0f613 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/gcs/BucketUtilsTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/gcs/BucketUtilsTest.java @@ -5,7 +5,7 @@ import java.nio.file.Path; import java.nio.file.Paths; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/haplotype/HaplotypeBAMWriterUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/haplotype/HaplotypeBAMWriterUnitTest.java index 613612a2e21..c88b1f7a3fa 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/haplotype/HaplotypeBAMWriterUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/haplotype/HaplotypeBAMWriterUnitTest.java @@ -12,7 +12,7 @@ import java.nio.file.Path; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.broadinstitute.hellbender.utils.genotyper.AlleleList; import org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList; import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods; @@ -21,7 +21,7 @@ import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; import org.broadinstitute.hellbender.utils.SimpleInterval; -import org.broadinstitute.hellbender.utils.test.SamAssertionUtils; +import org.broadinstitute.hellbender.testutils.SamAssertionUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/hdf5/HDF5LibraryUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/hdf5/HDF5LibraryUnitTest.java index 8e65bd4dda1..c899f692886 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/hdf5/HDF5LibraryUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/hdf5/HDF5LibraryUnitTest.java @@ -11,7 +11,6 @@ import org.broadinstitute.hdf5.HDF5Library; import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.BaseTest; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/DocumentationGenerationIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/utils/help/DocumentationGenerationIntegrationTest.java similarity index 95% rename from src/test/java/org/broadinstitute/hellbender/utils/test/DocumentationGenerationIntegrationTest.java rename to src/test/java/org/broadinstitute/hellbender/utils/help/DocumentationGenerationIntegrationTest.java index 9df6f4a5c35..ee9026d947c 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/DocumentationGenerationIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/help/DocumentationGenerationIntegrationTest.java @@ -1,9 +1,7 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.utils.help; import org.broadinstitute.hellbender.CommandLineProgramTest; -import org.broadinstitute.hellbender.utils.help.GATKHelpDoclet; import org.broadinstitute.hellbender.utils.runtime.ProcessController; -import org.testng.Assert; import org.testng.annotations.Test; import java.io.File; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/test/TabCompletionIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/utils/help/TabCompletionIntegrationTest.java similarity index 98% rename from src/test/java/org/broadinstitute/hellbender/utils/test/TabCompletionIntegrationTest.java rename to src/test/java/org/broadinstitute/hellbender/utils/help/TabCompletionIntegrationTest.java index 71d46373046..de5593d0b8d 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/test/TabCompletionIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/help/TabCompletionIntegrationTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.utils.help; import org.broadinstitute.barclay.argparser.ClassFinder; import org.broadinstitute.barclay.help.BashTabCompletionDoclet; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/io/IOUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/io/IOUtilsUnitTest.java index 34e74fe4823..82ed8b33c2f 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/io/IOUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/io/IOUtilsUnitTest.java @@ -4,8 +4,8 @@ import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.BaseTest; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.BaseTest; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; import org.testng.Assert; import org.testng.SkipException; import org.testng.annotations.DataProvider; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/nio/XorWrapperTest.java b/src/test/java/org/broadinstitute/hellbender/utils/nio/XorWrapperTest.java index 981095e1924..54131902913 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/nio/XorWrapperTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/nio/XorWrapperTest.java @@ -1,6 +1,6 @@ package org.broadinstitute.hellbender.utils.nio; -import org.broadinstitute.hellbender.utils.test.XorWrapper; +import org.broadinstitute.hellbender.testutils.XorWrapper; import org.testng.annotations.Test; import org.testng.Assert; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/python/PythonScriptExecutorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/python/PythonScriptExecutorUnitTest.java index 0584bd84f91..2c3f1bdd987 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/python/PythonScriptExecutorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/python/PythonScriptExecutorUnitTest.java @@ -2,7 +2,7 @@ import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/read/CigarUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/read/CigarUtilsUnitTest.java index 8d4729a59a7..abf6aa7ae1e 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/read/CigarUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/read/CigarUtilsUnitTest.java @@ -7,7 +7,7 @@ import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.Pair; import org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner; -import org.broadinstitute.hellbender.utils.test.ReadClipperTestUtils; +import org.broadinstitute.hellbender.testutils.ReadClipperTestUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/read/markduplicates/MarkDuplicatesSparkTester.java b/src/test/java/org/broadinstitute/hellbender/utils/read/markduplicates/MarkDuplicatesSparkTester.java index baf4021aeb7..888bf81b352 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/read/markduplicates/MarkDuplicatesSparkTester.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/read/markduplicates/MarkDuplicatesSparkTester.java @@ -4,7 +4,7 @@ import org.broadinstitute.hellbender.cmdline.CommandLineProgram; import org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection; import org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark; -import org.broadinstitute.hellbender.utils.test.testers.AbstractMarkDuplicatesTester; +import org.broadinstitute.hellbender.testutils.testers.AbstractMarkDuplicatesTester; /** * A tester class for {@link MarkDuplicatesSpark}. diff --git a/src/test/java/org/broadinstitute/hellbender/utils/read/markduplicates/MarkDuplicatesTester.java b/src/test/java/org/broadinstitute/hellbender/utils/read/markduplicates/MarkDuplicatesTester.java index 3ffdbc12d57..f7a83b534b7 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/read/markduplicates/MarkDuplicatesTester.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/read/markduplicates/MarkDuplicatesTester.java @@ -4,7 +4,7 @@ import htsjdk.samtools.ValidationStringency; import org.broadinstitute.hellbender.cmdline.CommandLineProgram; import org.broadinstitute.hellbender.tools.walkers.markduplicates.MarkDuplicatesGATK; -import org.broadinstitute.hellbender.utils.test.testers.AbstractMarkDuplicatesTester; +import org.broadinstitute.hellbender.testutils.testers.AbstractMarkDuplicatesTester; /** * This class is an extension of AbstractMarkDuplicatesCommandLineProgramTester used to test MarkDuplicatesGATK with SAM files generated on the fly. diff --git a/src/test/java/org/broadinstitute/hellbender/utils/recalibration/QualQuantizerUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/recalibration/QualQuantizerUnitTest.java index 33771505d7a..842d31ddae7 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/recalibration/QualQuantizerUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/recalibration/QualQuantizerUnitTest.java @@ -3,7 +3,7 @@ import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.utils.QualityUtils; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/runtime/StreamingProcessControllerUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/runtime/StreamingProcessControllerUnitTest.java index 00f50106f0e..6884ca7038f 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/runtime/StreamingProcessControllerUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/runtime/StreamingProcessControllerUnitTest.java @@ -1,6 +1,6 @@ package org.broadinstitute.hellbender.utils.runtime; -import org.broadinstitute.hellbender.utils.test.BaseTest; +import org.broadinstitute.hellbender.testutils.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/spark/SparkUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/spark/SparkUtilsUnitTest.java index 0d72e7b8a54..53945383b1d 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/spark/SparkUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/spark/SparkUtilsUnitTest.java @@ -18,7 +18,7 @@ import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.read.ReadCoordinateComparator; import org.broadinstitute.hellbender.utils.read.ReadQueryNameComparator; -import org.broadinstitute.hellbender.utils.test.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtilsUnitTest.java index ce495cef242..55644f885d9 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtilsUnitTest.java @@ -18,7 +18,7 @@ import org.broadinstitute.hellbender.engine.FeatureManager; import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod; import org.broadinstitute.hellbender.utils.*; -import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; @@ -1538,7 +1538,7 @@ public void remove() { } }; } - + @Test(dataProvider = "totalPloidyData") public void testTotalPloidy(final int[] ploidies, final int defaultPloidy, final int expected) { final Genotype[] genotypes = new Genotype[ploidies.length]; diff --git a/src/test/java/org/broadinstitute/hellbender/utils/variant/writers/GVCFWriterUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/variant/writers/GVCFWriterUnitTest.java index f3c2fdcc08f..84999f4cd6f 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/variant/writers/GVCFWriterUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/variant/writers/GVCFWriterUnitTest.java @@ -15,7 +15,7 @@ import org.broadinstitute.hellbender.utils.SimpleInterval; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec; +import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilder.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilder.java similarity index 98% rename from src/main/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilder.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilder.java index 05abbf43de5..f39c86b170e 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilder.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/ArgumentsBuilder.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import org.apache.commons.lang3.StringUtils; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; @@ -154,7 +154,7 @@ public ArgumentsBuilder add(Object arg) { } /** - * @return the arguments as List + * @return the arguments as List */ public List getArgsList(){ return this.args; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/BaseTest.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java similarity index 99% rename from src/main/java/org/broadinstitute/hellbender/utils/test/BaseTest.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java index 165c7040b30..fceafb6e552 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/BaseTest.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import htsjdk.samtools.util.Log; import org.apache.logging.log4j.LogManager; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/CommandLineProgramTester.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/CommandLineProgramTester.java similarity index 95% rename from src/main/java/org/broadinstitute/hellbender/utils/test/CommandLineProgramTester.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/CommandLineProgramTester.java index dbed8e13d1c..d5941ccc36a 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/CommandLineProgramTester.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/CommandLineProgramTester.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import htsjdk.samtools.util.Log; import org.broadinstitute.hellbender.Main; @@ -26,7 +26,7 @@ public interface CommandLineProgramTester { * * Default behaviour uses {@link #makeCommandLineArgs(List, String)} with the tool name provided by {@link #getTestedToolName()}. * - * @param args List of command line arguments + * @param args List of command line arguments * @return String[] of command line arguments */ default String[] makeCommandLineArgs(final List args) { @@ -39,7 +39,7 @@ default String[] makeCommandLineArgs(final List args) { * * Default behaviour generates a command line in the form "toolname args", with the verbosity parameter returned by {@link #injectDefaultVerbosity(List)}. * - * @param args List of command line arguments + * @param args List of command line arguments * @param toolname name of the tool to test * @return String[] of command line arguments */ diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/FakeReferenceSource.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/FakeReferenceSource.java similarity index 95% rename from src/main/java/org/broadinstitute/hellbender/utils/test/FakeReferenceSource.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/FakeReferenceSource.java index 177facef40d..bab5d6bf2cd 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/FakeReferenceSource.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/FakeReferenceSource.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import org.apache.commons.lang3.StringUtils; import org.broadinstitute.hellbender.utils.SimpleInterval; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/GenomicsDBTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java similarity index 97% rename from src/main/java/org/broadinstitute/hellbender/utils/test/GenomicsDBTestUtils.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java index 835d4ab113f..985e911d51f 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/GenomicsDBTestUtils.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/GenomicsDBTestUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import htsjdk.samtools.util.Locatable; import org.broadinstitute.hellbender.engine.FeatureDataSource; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/IntegrationTestSpec.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/IntegrationTestSpec.java similarity index 99% rename from src/main/java/org/broadinstitute/hellbender/utils/test/IntegrationTestSpec.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/IntegrationTestSpec.java index 6d493a6d3d8..c67834ce571 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/IntegrationTestSpec.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/IntegrationTestSpec.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import htsjdk.samtools.ValidationStringency; import org.apache.commons.lang3.StringUtils; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/MiniClusterUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/MiniClusterUtils.java similarity index 98% rename from src/main/java/org/broadinstitute/hellbender/utils/test/MiniClusterUtils.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/MiniClusterUtils.java index 77020e73bb6..0e5bca3686f 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/MiniClusterUtils.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/MiniClusterUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/ReadClipperTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/ReadClipperTestUtils.java similarity index 97% rename from src/main/java/org/broadinstitute/hellbender/utils/test/ReadClipperTestUtils.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/ReadClipperTestUtils.java index 0208b607686..894a1d82ec1 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/ReadClipperTestUtils.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/ReadClipperTestUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import htsjdk.samtools.*; import org.broadinstitute.hellbender.utils.read.ArtificialReadUtils; @@ -83,7 +83,7 @@ public static List generateCigarList(int maximumLength) { * A valid cigar object obeys the following rules: * - No Hard/Soft clips in the middle of the read * - No deletions in the beginning / end of the read - * - No repeated adjacent element (e.g. 1M2M -> this should be 3M) + * - No repeated adjacent element (e.g. 1M2M, this should be 3M) * - No consecutive I/D elements * * @param maximumCigarElements the maximum number of elements in the cigar diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/ReadsPreprocessingPipelineTestData.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/ReadsPreprocessingPipelineTestData.java similarity index 99% rename from src/main/java/org/broadinstitute/hellbender/utils/test/ReadsPreprocessingPipelineTestData.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/ReadsPreprocessingPipelineTestData.java index b1ba5d4c731..6a0c3510823 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/ReadsPreprocessingPipelineTestData.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/ReadsPreprocessingPipelineTestData.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import com.google.common.collect.Lists; import htsjdk.samtools.SAMRecord; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/SamAssertionUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/SamAssertionUtils.java similarity index 99% rename from src/main/java/org/broadinstitute/hellbender/utils/test/SamAssertionUtils.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/SamAssertionUtils.java index c642c235d43..e638aa4408d 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/SamAssertionUtils.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/SamAssertionUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import com.google.common.collect.Sets; import htsjdk.samtools.SAMFileHeader; @@ -131,7 +131,7 @@ public static void assertSamValid(final File sam) throws IOException { /** * Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes). * Returns null if the files are considered equals and returns a String describing the reason for comparison failure. - * The lenient comparison only checks headers and alignment info {@see SamComparison}. Compares headers, and if headers are compatible enough, compares SAMRecords, + * The lenient comparison only checks headers and alignment info {@link SamComparison}. Compares headers, and if headers are compatible enough, compares SAMRecords, * looking only at basic alignment info. */ public static String samsEqualLenient(final File actualSam, final File expectedSam, final ValidationStringency validation, final File reference) throws IOException { diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/SparkTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/SparkTestUtils.java similarity index 96% rename from src/main/java/org/broadinstitute/hellbender/utils/test/SparkTestUtils.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/SparkTestUtils.java index 05625f38285..8e624fd1dfb 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/SparkTestUtils.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/SparkTestUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import org.apache.spark.SparkConf; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/VariantContextTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java similarity index 98% rename from src/main/java/org/broadinstitute/hellbender/utils/test/VariantContextTestUtils.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java index 7c9f7487466..c0c226bb5fc 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/VariantContextTestUtils.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java @@ -1,12 +1,10 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import com.google.common.annotations.VisibleForTesting; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFConstants; -import com.google.common.collect.BiMap; -import com.google.common.collect.HashBiMap; import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.*; import org.apache.commons.collections4.CollectionUtils; @@ -20,10 +18,7 @@ import org.broadinstitute.hellbender.tools.walkers.annotator.Annotation; import org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils; import org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod; -import org.broadinstitute.hellbender.utils.MathUtils; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.collections.Permutation; -import org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; import org.testng.Assert; @@ -98,7 +93,7 @@ static Object normalizeToInteger(final Object attribute) { } catch ( final NumberFormatException e) { return attribute; } - } + } return attribute; } @@ -122,7 +117,7 @@ static Object normalizeScientificNotation(final Object attribute){ return Arrays.stream(split).map( s -> {return Arrays.stream(s.split(",",-1)) .map(d -> {if (d.equals("")) return d; - else return Double.toString(Double.parseDouble(d));}) + else return Double.toString(Double.parseDouble(d));}) .collect(Collectors.joining(","));}) .collect(Collectors.joining("|")); } else { @@ -159,7 +154,7 @@ public static VariantContext sortAlleles(final VariantContext vc, final VCFHeade result.alleles(sortedAlleles); GenotypesContext newGT = AlleleSubsettingUtils.subsetAlleles(vc.getGenotypes(),2,vc.getAlleles(),sortedAlleles, - GenotypeAssignmentMethod.SET_TO_NO_CALL, vc.getAttributeAsInt(VCFConstants.DEPTH_KEY,0)); + GenotypeAssignmentMethod.SET_TO_NO_CALL, vc.getAttributeAsInt(VCFConstants.DEPTH_KEY,0)); // Asserting that the new genotypes were calculated properly in case AlleleSubsettingUtils behavior changes if (newGT.getSampleNames().size() != vc.getGenotypes().size()) throw new IllegalStateException("Sorting this variant context resulted in a different number of genotype alleles, check that AlleleSubsettingUtils still supports reordering:" + vc.toString()); diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/XorWrapper.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/XorWrapper.java similarity index 97% rename from src/main/java/org/broadinstitute/hellbender/utils/test/XorWrapper.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/XorWrapper.java index 992506960e9..27f9135ded6 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/XorWrapper.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/XorWrapper.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.utils.test; +package org.broadinstitute.hellbender.testutils; import com.google.common.annotations.VisibleForTesting; import java.io.IOException; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/test/testers/SamFileTester.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/testers/SamFileTester.java similarity index 94% rename from src/main/java/org/broadinstitute/hellbender/utils/test/testers/SamFileTester.java rename to src/testUtils/java/org/broadinstitute/hellbender/testutils/testers/SamFileTester.java index 1627503bd1e..51774a4656e 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/test/testers/SamFileTester.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/testers/SamFileTester.java @@ -1,11 +1,11 @@ -package org.broadinstitute.hellbender.utils.test.testers; +package org.broadinstitute.hellbender.testutils.testers; import htsjdk.samtools.*; import htsjdk.samtools.util.CloseableIterator; import htsjdk.samtools.util.IOUtil; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; +import org.broadinstitute.hellbender.testutils.CommandLineProgramTester; import org.testng.Assert; -import org.broadinstitute.hellbender.utils.test.CommandLineProgramTester; import java.io.File; import java.util.*; @@ -97,7 +97,7 @@ public File getOutputDir() { private void setOutputDir() { this.outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".", ".tmp"); if (deleteOnExit) { - outputDir.deleteOnExit(); + outputDir.deleteOnExit(); } } @@ -186,7 +186,7 @@ public void addMappedPair(final int referenceSequenceIndex, final boolean isDuplicate2, final int defaultQualityScore) { addMappedPair(referenceSequenceIndex, alignmentStart1, alignmentStart2, isDuplicate1, isDuplicate2, null, null, - false, defaultQualityScore); + false, defaultQualityScore); } public void addMappedPair(final int referenceSequenceIndex, @@ -199,7 +199,7 @@ public void addMappedPair(final int referenceSequenceIndex, final boolean firstOnly, final int defaultQualityScore) { addMappedPair(referenceSequenceIndex, alignmentStart1, alignmentStart2, isDuplicate1, isDuplicate2, cigar1, - cigar2, false, true, firstOnly, defaultQualityScore); + cigar2, false, true, firstOnly, defaultQualityScore); } public void addMappedPair(final int referenceSequenceIndex, @@ -214,7 +214,7 @@ public void addMappedPair(final int referenceSequenceIndex, final boolean firstOnly, final int defaultQualityScore) { addMatePair(referenceSequenceIndex, alignmentStart1, alignmentStart2, false, false, isDuplicate1, isDuplicate2, cigar1, cigar2, - strand1, strand2, firstOnly, false, false, defaultQualityScore); + strand1, strand2, firstOnly, false, false, defaultQualityScore); } public void addMatePair(final int referenceSequenceIndex, @@ -233,14 +233,14 @@ public void addMatePair(final int referenceSequenceIndex, final boolean record2NonPrimary, final int defaultQualityScore) { addMatePair("READ" + readNameCounter++, referenceSequenceIndex, alignmentStart1, alignmentStart2, record1Unmapped, record2Unmapped, - isDuplicate1, isDuplicate2, cigar1, cigar2, strand1, strand2, firstOnly, record1NonPrimary, record2NonPrimary, - defaultQualityScore); + isDuplicate1, isDuplicate2, cigar1, cigar2, strand1, strand2, firstOnly, record1NonPrimary, record2NonPrimary, + defaultQualityScore); } private void addFragment(final int referenceSequenceIndex, final int alignmentStart, final boolean recordUnmapped, final boolean isDuplicate, final String cigar, final String qualityString, final int defaultQualityScore, final boolean isSecondary) { addFragment("READ" + readNameCounter++, referenceSequenceIndex, alignmentStart, recordUnmapped, isDuplicate, cigar, - qualityString, defaultQualityScore, isSecondary, false); + qualityString, defaultQualityScore, isSecondary, false); } private void addFragment(final String readName, final int referenceSequenceIndex, final int alignmentStart, final boolean recordUnmapped, final boolean isDuplicate, final String cigar, @@ -273,7 +273,7 @@ public void addMatePair(final String readName, final int defaultQuality, final String readGroup) { final List samRecordList = samRecordSetBuilder.addPair(readName, referenceSequenceIndex1, referenceSequenceIndex2, alignmentStart1, alignmentStart2, - record1Unmapped, record2Unmapped, cigar1, cigar2, strand1, strand2, record1NonPrimary, record2NonPrimary, defaultQuality); + record1Unmapped, record2Unmapped, cigar1, cigar2, strand1, strand2, record1NonPrimary, record2NonPrimary, defaultQuality); final SAMRecord record1 = samRecordList.get(0); final SAMRecord record2 = samRecordList.get(1); @@ -316,7 +316,7 @@ public void addMatePair(final String readName, final boolean record2NonPrimary, final int defaultQuality) { addMatePair(readName, referenceSequenceIndex,referenceSequenceIndex, alignmentStart1, alignmentStart2, record1Unmapped, record2Unmapped, - isDuplicate1, isDuplicate2, cigar1, cigar2, strand1, strand2, firstOnly, record1NonPrimary, record2NonPrimary, defaultQuality, "1"); + isDuplicate1, isDuplicate2, cigar1, cigar2, strand1, strand2, firstOnly, record1NonPrimary, record2NonPrimary, defaultQuality, "1"); } protected abstract void test();