/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/ |
H A D | UnmarkDuplicatesIntegrationTest.java | 32 …public void testUnmarkDuplicates(String samFile, int duplicateCount, File referenceFile) throws IO… in testUnmarkDuplicates() argument 34 …Assert.assertEquals(getDuplicateCountForBam(inputBam, referenceFile), duplicateCount, "Wrong numbe… in testUnmarkDuplicates() 41 if(referenceFile != null) { in testUnmarkDuplicates() 42 args.addReference(referenceFile); in testUnmarkDuplicates() 47 …Assert.assertEquals(getDuplicateCountForBam(outputBam, referenceFile), 0, "Duplicates still presen… in testUnmarkDuplicates() 50 …private static int getDuplicateCountForBam(final File bam, final File referenceFile) throws IOExce… in getDuplicateCountForBam() argument 53 if(referenceFile != null) { in getDuplicateCountForBam() 54 factory.referenceSequence(referenceFile); in getDuplicateCountForBam()
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/dports/net/messagelib/messagelib-21.12.3/messagecomposer/autotests/ |
H A D | autocryptheadersjobtest.cpp | 76 auto referenceFile = QStringLiteral("autcryptheader.mbox"); in testAutocryptHeader() local 77 QFile f(referenceFile); in testAutocryptHeader() 83 Test::compareFile(referenceFile, QStringLiteral(MAIL_DATA_DIR "/") + referenceFile); in testAutocryptHeader() 120 auto referenceFile = QStringLiteral("autcryptheader.mbox"); in testContentChained() local 121 QFile f(referenceFile); in testContentChained() 127 Test::compareFile(referenceFile, QStringLiteral(MAIL_DATA_DIR "/") + referenceFile); in testContentChained() 166 auto referenceFile = QStringLiteral("autocryptgossipheader.mbox"); in testAutocryptGossipHeader() local 167 Test::compareFile(&content, QStringLiteral(MAIL_DATA_DIR "/") + referenceFile); in testAutocryptGossipHeader() 226 auto referenceFile = QStringLiteral("autocryptgossipheader.mbox"); in testSetGnupgHome() local 227 Test::compareFile(&content, QStringLiteral(MAIL_DATA_DIR "/") + referenceFile); in testSetGnupgHome() [all …]
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/dports/devel/qtcreator/qt-creator-opensource-src-5.0.3/src/plugins/cpptools/ |
H A D | symbolfinder.cpp | 460 if (m_filePriorityCache.contains(referenceFile)) { in fileIterationOrder() 461 checkCacheConsistency(referenceFile, snapshot); in fileIterationOrder() 464 insertCache(referenceFile, doc->fileName()); in fileIterationOrder() 469 trackCacheUse(referenceFile); in fileIterationOrder() 489 insertCache(referenceFile, doc->fileName()); in checkCacheConsistency() 504 m_fileMetaCache[referenceFile].remove(comparingFile); in clearCache() 512 order.setReference(referenceFile, projectPartId); in insertCache() 516 m_fileMetaCache[referenceFile].insert(comparingFile); in insertCache() 522 if (m_recent.last() == referenceFile) in trackCacheUse() 524 m_recent.removeOne(referenceFile); in trackCacheUse() [all …]
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H A D | symbolfinder.h | 76 QStringList fileIterationOrder(const QString &referenceFile, 78 void checkCacheConsistency(const QString &referenceFile, const CPlusPlus::Snapshot &snapshot); 79 void clearCache(const QString &referenceFile, const QString &comparingFile); 80 void insertCache(const QString &referenceFile, const QString &comparingFile); 82 void trackCacheUse(const QString &referenceFile);
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/dports/sysutils/chaoskube/chaoskube-0.22.0/vendor/github.com/googleapis/gnostic/plugins/ |
H A D | plugins_test.go | 24 func testPlugin(t *testing.T, plugin string, inputFile string, outputFile string, referenceFile str… 38 err = exec.Command("diff", outputFile, referenceFile).Run() 40 t.Logf("Diff failed: %s vs %s %+v", outputFile, referenceFile, err) 75 referenceFile := "../testdata/errors/invalid-plugin-invocation.errors" 76 err = exec.Command("diff", outputFile, referenceFile).Run() 78 t.Logf("Diff failed: %s vs %s %+v", outputFile, referenceFile, err)
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/dports/net-mgmt/prometheus2/prometheus-2.30.3/vendor/github.com/googleapis/gnostic/plugins/ |
H A D | plugins_test.go | 24 func testPlugin(t *testing.T, plugin string, inputFile string, outputFile string, referenceFile str… 38 err = exec.Command("diff", outputFile, referenceFile).Run() 40 t.Logf("Diff failed: %s vs %s %+v", outputFile, referenceFile, err) 75 referenceFile := "../testdata/errors/invalid-plugin-invocation.errors" 76 err = exec.Command("diff", outputFile, referenceFile).Run() 78 t.Logf("Diff failed: %s vs %s %+v", outputFile, referenceFile, err)
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/dports/sysutils/helm/helm-3.5.2/vendor/github.com/googleapis/gnostic/plugins/ |
H A D | plugins_test.go | 24 func testPlugin(t *testing.T, plugin string, inputFile string, outputFile string, referenceFile str… 38 err = exec.Command("diff", outputFile, referenceFile).Run() 40 t.Logf("Diff failed: %s vs %s %+v", outputFile, referenceFile, err) 75 referenceFile := "../testdata/errors/invalid-plugin-invocation.errors" 76 err = exec.Command("diff", outputFile, referenceFile).Run() 78 t.Logf("Diff failed: %s vs %s %+v", outputFile, referenceFile, err)
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/dports/devel/gitlab-runner/gitlab-runner-8925d9a06fd8e452e2161a768462652a2a13111f/vendor/github.com/googleapis/gnostic/gnostic-0.4.1/plugins/ |
H A D | plugins_test.go | 24 func testPlugin(t *testing.T, plugin string, inputFile string, outputFile string, referenceFile str… 38 err = exec.Command("diff", outputFile, referenceFile).Run() 40 t.Logf("Diff failed: %s vs %s %+v", outputFile, referenceFile, err) 75 referenceFile := "../testdata/errors/invalid-plugin-invocation.errors" 76 err = exec.Command("diff", outputFile, referenceFile).Run() 78 t.Logf("Diff failed: %s vs %s %+v", outputFile, referenceFile, err)
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/ |
H A D | SortSamSparkIntegrationTest.java | 69 File referenceFile = null == referenceFileName ? null : getTestFile(referenceFileName); in testSortBAMs() local 76 if (null != referenceFile) { in testSortBAMs() 77 args.addReference(referenceFile); in testSortBAMs() 78 factory.referenceSequence(referenceFile); in testSortBAMs() 85 …qual(actualOutputFile, expectedOutputFile, ValidationStringency.DEFAULT_STRINGENCY, referenceFile); in testSortBAMs() 103 File referenceFile = null == referenceFileName ? null : getTestFile(referenceFileName); in testSortBAMsSharded() local 107 if (null != referenceFile) { in testSortBAMsSharded() 108 args.addReference(referenceFile); in testSortBAMsSharded() 117 …w GATKPath(actualOutputFile.getAbsolutePath()), referenceFile == null ? null : new GATKPath(refere… in testSortBAMsSharded() 120 referenceFileName == null ? null : new GATKPath(referenceFile.getAbsolutePath())); in testSortBAMsSharded()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/validation/ |
H A D | CompareBaseQualitiesIntegrationTest.java | 42 final File referenceFile = new File(b37_reference_20_21); in makeCompareBasesProvider() local 48 {firstCram, secondCram, referenceFile, outFile, sq, "two.reads.qual.diff.txt"}, in makeCompareBasesProvider() 49 {firstBam, secondCram, referenceFile, outFile, sq, "two.reads.qual.diff.txt"}, in makeCompareBasesProvider() 50 {firstCram, secondBam, referenceFile, outFile, sq, "two.reads.qual.diff.txt"}, in makeCompareBasesProvider() 56 …public void singleReadDiffTest(File firstBam, File secondBam, File referenceFile, File outFile, Li… in singleReadDiffTest() argument 64 if (null != referenceFile) { in singleReadDiffTest() 66 args.addRaw(referenceFile.getAbsolutePath()); in singleReadDiffTest()
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/dports/www/tikiwiki/tiki-21.2/admin/ |
H A D | include_sefurl.php | 40 $referenceFile = fopen($referenceFileName, "r"); variable 41 if ($referenceFile) { 44 fgets($referenceFile); 47 $referenceIdLine = fgets($referenceFile); 70 fclose($referenceFile);
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/dports/devel/tclvfs/tclvfs-20080503/library/template/ |
H A D | deltavfs.tcl | 76 foreach referenceFile $referenceFiles { 77 regsub {\;vfs&delta[0-9]*$} $referenceFile "" reconFile] 78 set f [open $referenceFile r] 83 file delete $referenceFile 189 set referenceFile [lindex $nonDeltas $i] 194 file stat $referenceFile fileStats 197 set fileName $referenceFile\;vfs&delta 198 file rename $referenceFile $fileName 202 array set fileStats [file attributes $referenceFile] 204 set fileName $referenceFile\;vfs&delta$targetTimeStamp [all …]
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/dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.platform.team/tests/org.eclipse.team.tests.cvs.core/src/org/eclipse/team/tests/ccvs/core/compatible/ |
H A D | SameResultEnv.java | 247 String[] content1 = super.readFromFile(referenceFile); in readFromFile() 258 IResource referenceFile, eclipseFile; in deleteFile() local 260 referenceFile = referenceProject.findMember(relativeFileName); in deleteFile() 263 referenceFile = referenceProject; in deleteFile() 266 assertEquals(referenceFile != null, eclipseFile != null); in deleteFile() 267 if (referenceFile == null) return; in deleteFile() 268 assertEquals(referenceFile.exists(), eclipseFile.exists()); in deleteFile() 269 referenceFile.delete(true, null); in deleteFile() 294 appendToFile(referenceFile, contents); in appendToFile() 309 prefixToFile(referenceFile, contents); in prefixToFile() [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
H A D | ReadUtilsIntegrationTest.java | 44 final File referenceFile, in testCreatePathSAMWriter() argument 55 …try (final SamReader samReader = SamReaderFactory.makeDefault().referenceSequence(referenceFile).o… in testCreatePathSAMWriter() 62 final Path referencePath = referenceFile == null ? null : referenceFile.toPath(); in testCreatePathSAMWriter() 77 …try (final SamReader samReader = SamReaderFactory.makeDefault().referenceSequence(referenceFile).o… in testCreatePathSAMWriter() 78 …eader outputReader = SamReaderFactory.makeDefault().referenceSequence(referenceFile).open(outputPa… in testCreatePathSAMWriter()
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/dports/net-mgmt/thanos/thanos-0.11.0/vendor/github.com/googleapis/gnostic/ |
H A D | gnostic_test.go | 12 func testCompiler(t *testing.T, inputFile string, referenceFile string, expectErrors bool) { 13 outputFormat := filepath.Ext(referenceFile)[1:] 40 err = exec.Command("diff", testFile, referenceFile).Run() 51 func testNormal(t *testing.T, inputFile string, referenceFile string) { 52 testCompiler(t, inputFile, referenceFile, false) 55 func testErrors(t *testing.T, inputFile string, referenceFile string) { 56 testCompiler(t, inputFile, referenceFile, true) 125 func testPlugin(t *testing.T, plugin string, inputFile string, outputFile string, referenceFile str… 139 err = exec.Command("diff", outputFile, referenceFile).Run() 217 referenceFile := "test/library-example-with-ext.text.out" [all …]
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/dports/misc/concourse/concourse-6.7.2/vendor/github.com/googleapis/gnostic/ |
H A D | gnostic_test.go | 12 func testCompiler(t *testing.T, inputFile string, referenceFile string, expectErrors bool) { 13 outputFormat := filepath.Ext(referenceFile)[1:] 40 err = exec.Command("diff", testFile, referenceFile).Run() 51 func testNormal(t *testing.T, inputFile string, referenceFile string) { 52 testCompiler(t, inputFile, referenceFile, false) 55 func testErrors(t *testing.T, inputFile string, referenceFile string) { 56 testCompiler(t, inputFile, referenceFile, true) 125 func testPlugin(t *testing.T, plugin string, inputFile string, outputFile string, referenceFile str… 139 err = exec.Command("diff", outputFile, referenceFile).Run() 217 referenceFile := "test/library-example-with-ext.text.out" [all …]
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/dports/sysutils/istio/istio-1.6.7/vendor/github.com/googleapis/gnostic/ |
H A D | gnostic_test.go | 12 func testCompiler(t *testing.T, inputFile string, referenceFile string, expectErrors bool) { 13 outputFormat := filepath.Ext(referenceFile)[1:] 40 err = exec.Command("diff", testFile, referenceFile).Run() 51 func testNormal(t *testing.T, inputFile string, referenceFile string) { 52 testCompiler(t, inputFile, referenceFile, false) 55 func testErrors(t *testing.T, inputFile string, referenceFile string) { 56 testCompiler(t, inputFile, referenceFile, true) 125 func testPlugin(t *testing.T, plugin string, inputFile string, outputFile string, referenceFile str… 139 err = exec.Command("diff", outputFile, referenceFile).Run() 217 referenceFile := "test/library-example-with-ext.text.out" [all …]
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/dports/devel/qtcreator/qt-creator-opensource-src-5.0.3/scripts/ |
H A D | checkInstalledFiles.py | 35 def referenceFile(): function 50 f = open(referenceFile(), 'r'); 98 f = open(referenceFile(), 'w') 102 print "Do not forget to commit", referenceFile() 105 …nified_diff(readReferenceFile(), generateReference(rootdir), fromfile=referenceFile(), tofile="gen…
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/ |
H A D | ClipReadsIntegrationTest.java | 39 File referenceFile = null; in testClipper() local 41 referenceFile = new File(getTestDataDir(),reference); in testClipper() 43 args.add(referenceFile.getAbsolutePath()); in testClipper() 54 SamAssertionUtils.assertSamsEqual(expectedOutBam, outFileBam, referenceFile); in testClipper() 71 final String referenceFile = "valid.fasta"; // lives in tools test folder in clipOptions() local 87 …{cramFile, referenceFile, ".cram", "-" + ClipReads.Q_TRIMMING_THRESHOLD_SHORT_NAME + " 10", "QT_10… in clipOptions() 88 …{cramFile, referenceFile, ".cram", "-" + ClipReads.Q_TRIMMING_THRESHOLD_SHORT_NAME + " 10", "QT_10… in clipOptions()
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/dports/net-mgmt/prometheus2/prometheus-2.30.3/vendor/github.com/googleapis/gnostic/metrics/vocabulary/ |
H A D | vocabulary_test.go | 55 func testVocabularyOutput(t *testing.T, outputFile string, referenceFile string) { 56 err := exec.Command("diff", outputFile, referenceFile).Run() 58 t.Logf("Diff failed: %s vs %s %+v", outputFile, referenceFile, err) 224 referenceFile := "../../testdata/metrics/vocabulary/petstore-v2.json" 238 referenceData, err := ioutil.ReadFile(referenceFile) 253 referenceFile := "../../testdata/metrics/vocabulary/petstore-v3.json" 267 referenceData, err := ioutil.ReadFile(referenceFile) 282 referenceFile := "../../testdata/metrics/vocabulary/discovery.json" 296 referenceData, err := ioutil.ReadFile(referenceFile)
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/dports/deskutils/kdepim-addons/kdepim-addons-21.12.3/plugins/messageviewerheaderplugins/autotests/ |
H A D | utils.cpp | 36 QString referenceFile = QStringLiteral(HEADER_DATA_DIR "/"); in testHeaderFile() local 38 referenceFile += dir + QStringLiteral("/"); in testHeaderFile() 40 referenceFile += fName; in testHeaderFile() 42 QVERIFY(QFile(referenceFile).exists()); in testHeaderFile() 59 const QStringList args = QStringList() << QStringLiteral("-u") << fName << referenceFile; in testHeaderFile()
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/dports/sysutils/chaoskube/chaoskube-0.22.0/vendor/github.com/googleapis/gnostic/ |
H A D | gnostic_test.go | 27 func testCompiler(t *testing.T, inputFile string, referenceFile string, expectErrors bool) { 28 outputFormat := filepath.Ext(referenceFile)[1:] 51 err = exec.Command("diff", testFile, referenceFile).Run() 62 func testNormal(t *testing.T, inputFile string, referenceFile string) { 63 testCompiler(t, inputFile, referenceFile, false) 66 func testErrors(t *testing.T, inputFile string, referenceFile string) { 67 testCompiler(t, inputFile, referenceFile, true)
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/dports/sysutils/helm/helm-3.5.2/vendor/github.com/googleapis/gnostic/ |
H A D | gnostic_test.go | 27 func testCompiler(t *testing.T, inputFile string, referenceFile string, expectErrors bool) { 28 outputFormat := filepath.Ext(referenceFile)[1:] 51 err = exec.Command("diff", testFile, referenceFile).Run() 62 func testNormal(t *testing.T, inputFile string, referenceFile string) { 63 testCompiler(t, inputFile, referenceFile, false) 66 func testErrors(t *testing.T, inputFile string, referenceFile string) { 67 testCompiler(t, inputFile, referenceFile, true)
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/dports/devel/gitlab-runner/gitlab-runner-8925d9a06fd8e452e2161a768462652a2a13111f/vendor/github.com/googleapis/gnostic/gnostic-0.4.1/ |
H A D | gnostic_test.go | 27 func testCompiler(t *testing.T, inputFile string, referenceFile string, expectErrors bool) { 28 outputFormat := filepath.Ext(referenceFile)[1:] 51 err = exec.Command("diff", testFile, referenceFile).Run() 62 func testNormal(t *testing.T, inputFile string, referenceFile string) { 63 testCompiler(t, inputFile, referenceFile, false) 66 func testErrors(t *testing.T, inputFile string, referenceFile string) { 67 testCompiler(t, inputFile, referenceFile, true)
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/dports/security/vault/vault-1.8.2/vendor/github.com/googleapis/gnostic/ |
H A D | gnostic_test.go | 12 func testCompiler(t *testing.T, inputFile string, referenceFile string, expectErrors bool) { 39 err = exec.Command("diff", outputFile, referenceFile).Run() 50 func testNormal(t *testing.T, inputFile string, referenceFile string) { 51 testCompiler(t, inputFile, referenceFile, false) 54 func testErrors(t *testing.T, inputFile string, referenceFile string) { 55 testCompiler(t, inputFile, referenceFile, true) 124 func testPlugin(t *testing.T, plugin string, inputFile string, outputFile string, referenceFile str… 138 err = exec.Command("diff", outputFile, referenceFile).Run() 216 referenceFile := "test/library-example-with-ext.text.out" 236 err = exec.Command("diff", outputFile, referenceFile).Run()
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