diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java index 77a941dd1..485e3ddda 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java @@ -54,7 +54,10 @@ import org.testng.annotations.Test; import java.io.File; import java.io.IOException; import java.lang.reflect.Method; -import java.util.*; +import java.util.Collections; +import java.util.Iterator; +import java.util.LinkedList; +import java.util.List; import static org.testng.Assert.assertTrue; @@ -119,9 +122,8 @@ public class AnalyzeCovariatesIntegrationTest extends WalkerTest { @Test(enabled = true) public void testPdfGeneration() throws IOException { - final File pdfFile = File.createTempFile("ACTest",".pdf"); + final File pdfFile = createTempFile("ACTest", ".pdf"); pdfFile.delete(); - pdfFile.deleteOnExit(); final List md5 = Collections.emptyList(); final WalkerTestSpec spec = new WalkerTestSpec( @@ -144,10 +146,8 @@ public class AnalyzeCovariatesIntegrationTest extends WalkerTest { final String description) throws IOException { - final File pdfFile = File.createTempFile("ACTest",".pdf"); - pdfFile.deleteOnExit(); - final List md5 = Collections.emptyList(); final File afterFile = new File(TEST_DATA_DIR,afterFileName); + afterFile.deleteOnExit(); final WalkerTestSpec spec = new WalkerTestSpec( buildCommandLine(null,"%s",true,true,afterFile), 1,UserException.IncompatibleRecalibrationTableParameters.class); @@ -258,16 +258,8 @@ public class AnalyzeCovariatesIntegrationTest extends WalkerTest { final boolean useBQSRFile, final boolean useBeforeFile, final boolean useAfterFile) throws IOException { - final File csvFile = useCsvFile ? File.createTempFile("ACTest",".csv") : null; - final File pdfFile = usePdfFile ? File.createTempFile("ACTest",".pdf") : null; - - if (csvFile != null) { - csvFile.deleteOnExit(); - } - - if (pdfFile != null) { - pdfFile.deleteOnExit(); - } + final File csvFile = useCsvFile ? createTempFile("ACTest",".csv") : null; + final File pdfFile = usePdfFile ? createTempFile("ACTest",".pdf") : null; return buildCommandLine(csvFile == null ? null : csvFile.toString(), pdfFile == null ? null : pdfFile.toString(), diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java index effa6aba0..5906fbc6c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java @@ -46,8 +46,8 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; +import htsjdk.variant.variantcontext.Allele; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph; -import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.utils.haplotype.Haplotype; @@ -57,18 +57,11 @@ import org.broadinstitute.gatk.utils.pairhmm.FlexibleHMM; import org.broadinstitute.gatk.utils.pairhmm.PairHMM; import org.broadinstitute.gatk.utils.sam.ClippedGATKSAMRecord; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; -import org.testng.Reporter; import org.testng.SkipException; -import org.testng.annotations.AfterClass; -import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import java.io.File; -import java.io.IOException; -import java.io.PrintWriter; import java.util.*; /** @@ -86,29 +79,6 @@ public class ReadThreadingLikelihoodCalculationEngineUnitTest extends ActiveRegi private static FlexibleHMM hmm = new FastLoglessPairHMM((byte)10); - // for debugging purposes: - private static final boolean DUMP_LIKELIHOODS = false; - private PrintWriter likelihoodDumpWriter = null; - private File likelihoodDumpFile = null; - - - @BeforeClass - private void setUp() throws IOException { - if (DUMP_LIKELIHOODS) { - likelihoodDumpFile = File.createTempFile("rtlce-test", ".txt"); - Reporter.log("Dumping Likelihoods in file '" + likelihoodDumpFile + "'",true); - likelihoodDumpWriter = new PrintWriter(likelihoodDumpFile);//new FileWriter(f)); - } - } - - @AfterClass - private void tearDown() throws IOException { - if (DUMP_LIKELIHOODS) { - likelihoodDumpWriter.close(); - Reporter.log("Dumped Likelihoods in file '" + likelihoodDumpFile + "'", true); - } - } - @Test(dataProvider="activeRegionTestDataSets",enabled=false) public void testActiveRegionsDataSet(final ActiveRegionTestDataSet as, final int kmerSize, final int readLength, final String variation, final int readCount, final int regionSize, final byte bq, final byte iq, final byte dq) { super.testActiveRegionsDataSet(as,kmerSize,readLength,variation,readCount,regionSize,bq,iq,dq); @@ -156,7 +126,6 @@ public class ReadThreadingLikelihoodCalculationEngineUnitTest extends ActiveRegi final double loglessDiff = loglessA1Lk - loglessA2Lk; final double graphDiff = graphA1Lk - graphA2Lk; final double epsilon = calculateEpsilon(graphDiff,loglessDiff); - dumpLikelihoods(read,loglessA1Lk,loglessA2Lk,graphA1Lk,graphA2Lk,read.getReadString() + " " + a1.getBaseString() + " " + a2.getBaseString()); Assert.assertEquals(graphDiff,loglessDiff,epsilon,String.format("Delta(%f,%f) = %f > %f",graphDiff,loglessDiff,Math.abs(graphDiff - loglessDiff),epsilon)); } @@ -252,11 +221,6 @@ public class ReadThreadingLikelihoodCalculationEngineUnitTest extends ActiveRegi return false; } - private void dumpLikelihoods(final GATKSAMRecord read, final Double loglessA1lk, final Double loglessA2lk, final Double a1lk, final Double a2lk, final String hapString) { - if (!DUMP_LIKELIHOODS) return; - likelihoodDumpWriter.println(Utils.join("\t","" + loglessA1lk,"" + loglessA2lk,"" + a1lk,"" + a2lk,read.getReadName(),read.getReadString(),hapString)); - likelihoodDumpWriter.flush(); - } @DataProvider(name="readLikekihoodRatioTestData") public Iterator readLikelihoodRatioTestDataSets() { diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java index 70fe08745..105486df7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java @@ -273,16 +273,14 @@ public class BaseGraphUnitTest extends BaseTest { @Test public void testPrintEmptyGraph() throws Exception { - final File tmp = File.createTempFile("tmp", "dot"); - tmp.deleteOnExit(); + final File tmp = createTempFile("tmp", "dot"); new SeqGraph(11).printGraph(tmp, 10); new TestGraph().printGraph(tmp, 10); } @Test public void testComplexGraph() throws Exception { - final File tmp = File.createTempFile("tmp", "dot"); - tmp.deleteOnExit(); + final File tmp = createTempFile("tmp", "dot"); graph.printGraph(tmp, 10); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java index 4a6b26381..86452c4b3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java @@ -63,7 +63,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { @Test public void testSimpleVCFStreaming() throws IOException { // Create a FIFO. This seems to be the only way to create an interprocess FIFO in Java (java.nio.Pipe is intraprocess only). - File tmpFifo = File.createTempFile("vcfstreaming",""); + File tmpFifo = createTempFile("vcfstreaming", ""); Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()}); @@ -93,7 +93,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { @Test public void testVCFStreamingChain() throws IOException { // Create a FIFO. This seems to be the only way to create an interprocess FIFO in Java (java.nio.Pipe is intraprocess only). - File tmpFifo = File.createTempFile("vcfstreaming",""); + File tmpFifo = createTempFile("vcfstreaming",""); Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()}); String testFile = privateTestDir + "yri.trio.gatk.ug.head.vcf"; diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java index 47081b264..8980d3aa6 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java @@ -113,8 +113,7 @@ public class ReadMetricsUnitTest extends BaseTest { } private void createBAM(final List reads) throws IOException { - testBAM = File.createTempFile("TraverseActiveRegionsUnitTest", ".bam"); - testBAM.deleteOnExit(); + testBAM = createTempFile("TraverseActiveRegionsUnitTest", ".bam"); SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, testBAM); for (GATKSAMRecord read : reads ) { diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java index 747082508..29e267693 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java @@ -26,23 +26,21 @@ package org.broadinstitute.gatk.engine.datasources.reads; import htsjdk.samtools.*; -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.utils.commandline.Tags; import org.broadinstitute.gatk.engine.arguments.ValidationExclusion; import org.broadinstitute.gatk.engine.downsampling.DownsampleType; import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod; import org.broadinstitute.gatk.engine.filters.ReadFilter; import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation; +import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.commandline.Tags; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.ArtificialSingleSampleReadStream; +import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import org.testng.Assert; import java.io.File; -import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; @@ -154,14 +152,7 @@ public class ReadShardBalancerUnitTest extends BaseTest { 150, numUnmappedReads); - File testBAMFile; - try { - testBAMFile = File.createTempFile("SAMDataSourceFillShardBoundaryTest", ".bam"); - testBAMFile.deleteOnExit(); - } - catch ( IOException e ) { - throw new ReviewedGATKException(String.format("Failed to create temp bam file for test %s. %s", this, e.getMessage())); - } + final File testBAMFile = createTempFile("SAMDataSourceFillShardBoundaryTest", ".bam"); SAMFileWriter bamWriter = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(header, true, testBAMFile); for ( SAMRecord read : artificialReads ) { diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java index ec12f7df8..a64773af8 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/refdata/tracks/RMDTrackBuilderUnitTest.java @@ -129,9 +129,8 @@ public class RMDTrackBuilderUnitTest extends BaseTest { */ private File createTempVCFFileAndIndex( final File vcfFile, final boolean createOutOfDateIndex ) { try { - final File tmpFile = File.createTempFile("RMDTrackBuilderUnitTest", ""); + final File tmpFile = createTempFile("RMDTrackBuilderUnitTest", ""); final File tmpIndex = Tribble.indexFile(tmpFile); - tmpFile.deleteOnExit(); tmpIndex.deleteOnExit(); copyFile(vcfFile, tmpFile); diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java index 42c458f91..918cb50dc 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java @@ -133,8 +133,7 @@ public class TraverseActiveRegionsUnitTest extends BaseTest { } private void createBAM(List reads) throws IOException { - testBAM = File.createTempFile("TraverseActiveRegionsUnitTest", ".bam"); - testBAM.deleteOnExit(); + testBAM = createTempFile("TraverseActiveRegionsUnitTest", ".bam"); SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, testBAM); for (GATKSAMRecord read : ReadUtils.sortReadsByCoordinate(reads)) { diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java index eeb3e0de6..4434e4464 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java @@ -25,26 +25,25 @@ package org.broadinstitute.gatk.engine.walkers; -import org.apache.commons.lang.StringUtils; import htsjdk.tribble.Tribble; import htsjdk.tribble.index.Index; import htsjdk.tribble.index.IndexFactory; -import htsjdk.tribble.index.tabix.TabixFormat; import htsjdk.tribble.util.TabixUtils; +import htsjdk.variant.bcf2.BCF2Utils; +import htsjdk.variant.vcf.VCFCodec; +import org.apache.commons.lang.StringUtils; +import org.broadinstitute.gatk.engine.CommandLineExecutable; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.phonehome.GATKRunReport; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.MD5DB; import org.broadinstitute.gatk.utils.MD5Mismatch; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.classloader.JVMUtils; -import org.broadinstitute.gatk.engine.CommandLineExecutable; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.phonehome.GATKRunReport; -import htsjdk.variant.bcf2.BCF2Utils; import org.broadinstitute.gatk.utils.collections.Pair; -import htsjdk.variant.vcf.VCFCodec; -import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.testng.Assert; import org.testng.annotations.AfterSuite; import org.testng.annotations.BeforeMethod; @@ -449,7 +448,7 @@ public class WalkerTest extends BaseTest { } - protected File createTempFileFromBase(String name) { + protected File createTempFileFromBase(final String name) { File fl = new File(name); fl.deleteOnExit(); return fl; diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java index af74beec6..447515d0e 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java @@ -67,12 +67,6 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { } } - public File createTempFileFromBase(String name) { - File fl = new File(name); - fl.deleteOnExit(); - return fl; - } - @Test public void testMapQ0Only() { String[] intervals = {"1:10,000,000-10,002,000","1:10,003,000-10,004,000"}; @@ -83,7 +77,7 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList()); // our base file - File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp"); + final File baseOutputFile = createTempFile("depthofcoveragemapq0",".tmp"); spec.setOutputFileLocation(baseOutputFile); spec.addAuxFile("f39af6ad99520fd4fb27b409ab0344a0",baseOutputFile); @@ -100,13 +94,13 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { @Test public void testLotsOfSamples() { - String[] intervals = {"1:1105290-1105295"}; - String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot3.CEU+TSI.5loci.bam"}; - String cmd = buildRootCmd(b36KGReference, new ArrayList(Arrays.asList(bams)), new ArrayList(Arrays.asList(intervals))); + final String[] intervals = {"1:1105290-1105295"}; + final String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot3.CEU+TSI.5loci.bam"}; + final String cmd = buildRootCmd(b36KGReference, new ArrayList(Arrays.asList(bams)), new ArrayList(Arrays.asList(intervals))); - WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList()); + final WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList()); - File baseOutputFile = this.createTempFile("testManySamples",".tmp"); + final File baseOutputFile = createTempFile("testManySamples",".tmp"); spec.setOutputFileLocation(baseOutputFile); spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile); diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java index 5b3f8595a..3da09fa85 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java @@ -69,14 +69,14 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { @Test public void testBaseOutputNoFiltering() { - String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"}; - String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"}; + final String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"}; + final String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"}; - String cmd = buildRootCmd(hg18Reference,new ArrayList(Arrays.asList(bams)),new ArrayList(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv -ct 10 -ct 15 -ct 20 -ct 25"; - WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList()); + final String cmd = buildRootCmd(hg18Reference,new ArrayList<>(Arrays.asList(bams)),new ArrayList<>(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv -ct 10 -ct 15 -ct 20 -ct 25"; + final WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList()); // our base file - File baseOutputFile = this.createTempFile("depthofcoveragenofiltering",".tmp"); + final File baseOutputFile = createTempFile("depthofcoveragenofiltering",".tmp"); spec.setOutputFileLocation(baseOutputFile); // now add the expected files that get generated @@ -111,7 +111,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { String cmd = buildRootCmd(hg18Reference,new ArrayList(Arrays.asList(bams)),new ArrayList(Arrays.asList(intervals))) + " -mmq 0 -mbq 5 --maxBaseQuality 4 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv"; WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList()); - File baseOutputFile = this.createTempFile("depthofcoveragenofiltering",".tmp"); + File baseOutputFile = createTempFile("depthofcoveragenofiltering",".tmp"); spec.setOutputFileLocation(baseOutputFile); spec.addAuxFile("6ccd7d8970ba98cb95fe41636a070c1c",baseOutputFile); diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java index 4090fced9..b8d60cf53 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java @@ -289,9 +289,9 @@ public abstract class BaseTest { * @param extension Extension to concat to the end of the file. * @return A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits. */ - public static File createTempFile(String name, String extension) { + public static File createTempFile(final String name, final String extension) { try { - File file = File.createTempFile(name, extension); + final File file = File.createTempFile(name, extension); file.deleteOnExit(); // Mark corresponding indices for deletion on exit as well just in case an index is created for the temp file: diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java index b6e67a961..f8aa1efbe 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java @@ -90,8 +90,7 @@ public class RodBindingCollectionUnitTest extends BaseTest { @Test public void testDefaultTagsInFile() throws IOException { - final File testFile = File.createTempFile("RodBindingCollectionUnitTest.defaultTags", ".list"); - testFile.deleteOnExit(); + final File testFile = createTempFile("RodBindingCollectionUnitTest.defaultTags", ".list"); final FileWriter writer = new FileWriter(testFile); writer.write(testVCFFileName, 0, testVCFFileName.length()); writer.close(); @@ -109,8 +108,7 @@ public class RodBindingCollectionUnitTest extends BaseTest { @Test(expectedExceptions = UserException.BadArgumentValue.class) public void testDuplicateEntriesInFile() throws IOException { - final File testFile = File.createTempFile("RodBindingCollectionUnitTest.variantListWithDuplicates", ".list"); - testFile.deleteOnExit(); + final File testFile = createTempFile("RodBindingCollectionUnitTest.variantListWithDuplicates", ".list"); final FileWriter writer = new FileWriter(testFile); writer.write(testVCFFileName + "\n"); writer.write(testVCFFileName + "\n"); @@ -121,16 +119,14 @@ public class RodBindingCollectionUnitTest extends BaseTest { @Test(expectedExceptions = UserException.BadArgumentValue.class) public void testValidateEmptyFile() throws IOException { - final File testFile = File.createTempFile("RodBindingCollectionUnitTest.emptyVCFList", ".list"); - testFile.deleteOnExit(); + final File testFile = createTempFile("RodBindingCollectionUnitTest.emptyVCFList", ".list"); ArgumentTypeDescriptor.getRodBindingsCollection(testFile, parsingEngine, VariantContext.class, "foo", mytags, "input"); } @Test public void testOverrideTagsInFile() throws IOException { - final File testFile = File.createTempFile("RodBindingCollectionUnitTest.overrideTags", ".list"); - testFile.deleteOnExit(); + final File testFile = createTempFile("RodBindingCollectionUnitTest.overrideTags", ".list"); final FileWriter writer = new FileWriter(testFile); final String textToWrite = "foo " + testVCFFileName; writer.write(textToWrite, 0, textToWrite.length()); diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java index 1c9607e3c..39be4582a 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java @@ -143,8 +143,7 @@ public class ListFileUtilsUnitTest extends BaseTest { } private File createTempListFile( String tempFilePrefix, String... lines ) throws Exception { - File tempListFile = File.createTempFile(tempFilePrefix, ".list"); - tempListFile.deleteOnExit(); + File tempListFile = createTempFile(tempFilePrefix, ".list"); PrintWriter out = new PrintWriter(tempListFile); for ( String line : lines ) {