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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/
H A DUnmarkDuplicatesIntegrationTest.java32 …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()
/dports/net/messagelib/messagelib-21.12.3/messagecomposer/autotests/
H A Dautocryptheadersjobtest.cpp76 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 …]
/dports/devel/qtcreator/qt-creator-opensource-src-5.0.3/src/plugins/cpptools/
H A Dsymbolfinder.cpp460 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 …]
H A Dsymbolfinder.h76 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);
/dports/sysutils/chaoskube/chaoskube-0.22.0/vendor/github.com/googleapis/gnostic/plugins/
H A Dplugins_test.go24 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)
/dports/net-mgmt/prometheus2/prometheus-2.30.3/vendor/github.com/googleapis/gnostic/plugins/
H A Dplugins_test.go24 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)
/dports/sysutils/helm/helm-3.5.2/vendor/github.com/googleapis/gnostic/plugins/
H A Dplugins_test.go24 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)
/dports/devel/gitlab-runner/gitlab-runner-8925d9a06fd8e452e2161a768462652a2a13111f/vendor/github.com/googleapis/gnostic/gnostic-0.4.1/plugins/
H A Dplugins_test.go24 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)
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/
H A DSortSamSparkIntegrationTest.java69 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()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/validation/
H A DCompareBaseQualitiesIntegrationTest.java42 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()
/dports/www/tikiwiki/tiki-21.2/admin/
H A Dinclude_sefurl.php40 $referenceFile = fopen($referenceFileName, "r"); variable
41 if ($referenceFile) {
44 fgets($referenceFile);
47 $referenceIdLine = fgets($referenceFile);
70 fclose($referenceFile);
/dports/devel/tclvfs/tclvfs-20080503/library/template/
H A Ddeltavfs.tcl76 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 …]
/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 DSameResultEnv.java247 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 …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/
H A DReadUtilsIntegrationTest.java44 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()
/dports/net-mgmt/thanos/thanos-0.11.0/vendor/github.com/googleapis/gnostic/
H A Dgnostic_test.go12 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 …]
/dports/misc/concourse/concourse-6.7.2/vendor/github.com/googleapis/gnostic/
H A Dgnostic_test.go12 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 …]
/dports/sysutils/istio/istio-1.6.7/vendor/github.com/googleapis/gnostic/
H A Dgnostic_test.go12 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 …]
/dports/devel/qtcreator/qt-creator-opensource-src-5.0.3/scripts/
H A DcheckInstalledFiles.py35 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…
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/
H A DClipReadsIntegrationTest.java39 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()
/dports/net-mgmt/prometheus2/prometheus-2.30.3/vendor/github.com/googleapis/gnostic/metrics/vocabulary/
H A Dvocabulary_test.go55 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)
/dports/deskutils/kdepim-addons/kdepim-addons-21.12.3/plugins/messageviewerheaderplugins/autotests/
H A Dutils.cpp36 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()
/dports/sysutils/chaoskube/chaoskube-0.22.0/vendor/github.com/googleapis/gnostic/
H A Dgnostic_test.go27 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)
/dports/sysutils/helm/helm-3.5.2/vendor/github.com/googleapis/gnostic/
H A Dgnostic_test.go27 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)
/dports/devel/gitlab-runner/gitlab-runner-8925d9a06fd8e452e2161a768462652a2a13111f/vendor/github.com/googleapis/gnostic/gnostic-0.4.1/
H A Dgnostic_test.go27 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)
/dports/security/vault/vault-1.8.2/vendor/github.com/googleapis/gnostic/
H A Dgnostic_test.go12 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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