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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/plotting/
H A DPlotDenoisedCopyRatiosIntegrationTest.java33 private void assertFilesCreated(final File outputDir) { in assertFilesCreated() argument
55 final File outputDir = createTempDir("testDir"); in testPlotting() local
64 assertFilesCreated(outputDir); in testPlotting()
70 final File outputDir = createTempDir("testDir"); in testPlottingInfiniteMaximumCopyRatio() local
80 assertFilesCreated(outputDir); in testPlottingInfiniteMaximumCopyRatio()
85 final File outputDir = createTempDir("testDir"); in testMinimumContigLength() local
98 final File outputDir = createTempDir("testDir"); in testNonExistentStandardizedFile() local
111 final File outputDir = createTempDir("testDir"); in testNonExistentDenoisedFile() local
124 final File outputDir = createTempDir("testDir"); in testNonExistentSequenceDictionaryFile() local
137 final File outputDir = createTempDir("testDir"); in testOutOfDictionaryBounds() local
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H A DPlotModeledSegmentsIntegrationTest.java41 final File outputDir = createTempDir("testDir"); in testPlotting() local
58 final File outputDir = createTempDir("testDir"); in testPlottingInfiniteMaximumCopyRatio() local
76 final File outputDir = createTempDir("testDir"); in testPlottingDenoisedCopyRatiosOnly() local
92 final File outputDir = createTempDir("testDir"); in testPlottingAllelicCountsOnly() local
107 final File outputDir = createTempDir("testDir"); in testMinimumContigLength() local
121 final File outputDir = createTempDir("testDir"); in testNonExistentDenoisedCopyRatiosFile() local
135 final File outputDir = createTempDir("testDir"); in testNonExistentAllelicCountsFile() local
149 final File outputDir = createTempDir("testDir"); in testNonExistentModeledSegmentsFile() local
163 final File outputDir = createTempDir("testDir"); in testNonExistentSequenceDictionaryFile() local
177 final File outputDir = createTempDir("testDir"); in testDenoisedCopyRatiosSampleNameMismatch() local
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/
H A DSplitIntervalsIntegrationTest.java37 final File outputDir = createTempDir("output"); in testOneInterval() local
43 .addOutput(outputDir); in testOneInterval()
53 final File outputDir = createTempDir("output"); in testOneIntervalAlternateExtension() local
60 .addOutput(outputDir); in testOneIntervalAlternateExtension()
70 final File outputDir = createTempDir("output"); in testSingleScatter() local
75 .addOutput(outputDir); in testSingleScatter()
86 final File outputDir = createTempDir("output"); in testTwoIntervals() local
92 .addOutput(outputDir); in testTwoIntervals()
111 .addOutput(outputDir); in testDontMixContigs()
124 .addOutput(outputDir); in testNoIntervals()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/
H A DModelSegmentsIntegrationTest.java50 .addOutput(outputDir) in testAllInputsAvailable()
63 .addOutput(outputDir) in testNoNormalAllelicCounts()
76 .addOutput(outputDir) in testNoDenoisedCopyRatios()
88 .addOutput(outputDir) in testAllelicCountsOnly()
100 .addOutput(outputDir) in testNoAllelicCounts()
161 .addOutput(outputDir) in testSampleNameMismatch()
173 .addOutput(outputDir) in testMissingSites()
186 .addOutput(outputDir) in testNonExistentDenoisedCopyRatiosFile()
199 .addOutput(outputDir) in testNonExistentAllelicCountsFile()
212 .addOutput(outputDir) in testNonExistentNormalAllelicCountsFile()
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/dports/www/phalcon4/cphalcon-4.1.1/tests/unit/Image/Adapter/Gd/
H A DWatermarkCest.php46 $outputDir = 'tests/image/gd';
48 $output = outputDir($outputDir . '/' . $outputImage);
59 outputDir($outputDir)
91 $outputDir = 'tests/image/gd';
93 $output = outputDir($outputDir . '/' . $outputImage);
102 outputDir($outputDir)
135 $outputDir = 'tests/image/gd';
137 $output = outputDir($outputDir . '/' . $outputImage);
148 outputDir($outputDir)
181 $output = outputDir($outputDir . '/' . $outputImage);
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H A DCropCest.php40 $outputDir = 'tests/image/gd';
44 $output = outputDir($outputDir . '/' . $cropImage);
48 $image->crop($width, $height)->save(outputDir($outputDir . '/' . $cropImage));
51 outputDir($outputDir)
89 $outputDir = 'tests/image/gd';
95 $output = outputDir($outputDir . '/' . $cropImage);
102 outputDir($outputDir)
H A DResizeCest.php40 $outputDir = 'tests/image/gd';
41 $output = outputDir($outputDir . '/resize.jpg');
50 outputDir($outputDir)
86 $outputDir = 'tests/image/gd';
87 $output = outputDir($outputDir . '/resize.png');
96 outputDir($outputDir)
/dports/devel/pear-phing/phing-2.6.1/tasks/ext/liquibase/
H A DLiquibaseDbDocTask.php32 protected $outputDir; variable in LiquibaseDbDocTask
40 public function setOutputDir($outputDir) argument
42 $this->outputDir = $outputDir;
53 if((null === $this->outputDir) or !is_dir($this->outputDir))
55 if(!mkdir($this->outputDir, 0777, true))
60 $this->outputDir
66 if(!is_writable($this->outputDir))
71 $this->outputDir
84 $this->execute('dbdoc', escapeshellarg($this->outputDir));
/dports/www/phalcon/cphalcon-3.4.5/build/_resource/Phalcon/Build/Generator/
H A DSafe.php22 protected $outputDir; variable in Phalcon\\Build\\Generator_Safe
61 * @param string $outputDir
63 public function __construct($rootDir, $outputDir) argument
66 $this->outputDir = $outputDir;
70 $this->phalconH = new Generator_File_PhalconH($this->sourceDir, $outputDir);
72 $this->configM4 = new Generator_File_ConfigM4($rootDir, $outputDir);
73 $this->configW32 = new Generator_File_ConfigW32($rootDir, $outputDir);
83 Util::cleanDirectory($this->outputDir);
100 copy($this->sourceDir . '/php_phalcon.h', $this->outputDir . '/php_phalcon.h');
111 foreach (file($this->outputDir . '/php_phalcon.h') as $line) {
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/dports/www/phalcon4/cphalcon-4.1.1/build/_resource/Phalcon/Build/Generator/
H A DSafe.php22 protected $outputDir; variable in Phalcon\\Build\\Generator_Safe
61 * @param string $outputDir
63 public function __construct($rootDir, $outputDir) argument
66 $this->outputDir = $outputDir;
70 $this->phalconH = new Generator_File_PhalconH($this->sourceDir, $outputDir);
72 $this->configM4 = new Generator_File_ConfigM4($rootDir, $outputDir);
73 $this->configW32 = new Generator_File_ConfigW32($rootDir, $outputDir);
83 Util::cleanDirectory($this->outputDir);
100 copy($this->sourceDir . '/php_phalcon.h', $this->outputDir . '/php_phalcon.h');
111 foreach (file($this->outputDir . '/php_phalcon.h') as $line) {
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/dports/biology/checkm/CheckM-1.0.18/scripts/
H A DgenomeTreeWorkflow.py45 def __init__(self, outputDir): argument
47 if os.path.exists(outputDir):
48 print '[Error] Output directory already exists: ' + outputDir
51 os.makedirs(outputDir)
58 self.hmmDir = os.path.join(outputDir, 'phylo_hmms')
59 self.alignmentDir = os.path.join(outputDir, 'gene_alignments')
60 self.geneTreeDir = os.path.join(outputDir, 'gene_trees')
62 self.finalGeneTreeDir = os.path.join(outputDir, 'gene_trees_final')
63 self.bootstrapDir = os.path.join(outputDir, 'bootstrap')
68 self.treeOut = os.path.join(outputDir, 'genome_tree.tre')
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/dports/graphics/ossim/ossim-OrchidIsland-2.11.1/apps/ossim-applanix2ogeom/
H A Dossim-applanix2ogeom.cpp40 const ossimFilename& outputDir);
122 ossimFilename outputDir; in main() local
131 if (outputDir.createDirectory() == false) in main()
140 outputDirOverrideFlag = outputDir.exists(); in main()
197 outputDir = imageToProcess.path(); in main()
199 processImage(eo, kwl, id, outputDir); in main()
206 if(!outputDir .isDir()) in main()
208 ossimFilename idFile = outputDir.file(); in main()
209 outputDir = outputDir.path(); in main()
301 if (outputDir != ossimFilename::NIL) in processImage()
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/dports/net/olsrd/olsrd-0.9.8/redhat/
H A Drunner22 outputDir="$scriptDir/generated"
23 specOutputFile="$outputDir/olsrd.spec"
144 "$outputDir/RPMS/"*.rpm "$outputDir/RPMS/"*.log
145 if [[ -d "$outputDir/RPMS" ]]; then
146 rmdir -v --ignore-fail-on-non-empty "$outputDir/RPMS"
148 if [[ -d "$outputDir" ]]; then
149 rmdir -v --ignore-fail-on-non-empty "$outputDir"
156 mkdir -p -v "$outputDir"
167 echo "Generating '$outputDir/$tarOutputFilename'"
172 > "$outputDir/$tarOutputFilename"
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/dports/devel/app-builder/app-builder-3.4.2/pkg/electron/
H A DelectronUnpack.go20 outputDir := command.Flag("output", "").Required().String()
29 return UnpackElectron(configs, *outputDir, *distMacOsAppName, true)
33 func UnpackElectron(configs []ElectronDownloadOptions, outputDir string, distMacOsAppName string, i…
38 return fsutil.EnsureEmptyDir(outputDir)
62 …excludedFiles[filepath.Join(outputDir, distMacOsAppName, "Contents", "Resources", "default_app.asa…
63 excludedFiles[filepath.Join(outputDir, "resources", "default_app.asar")] = true
65 …excludedFiles[filepath.Join(outputDir, distMacOsAppName, "Contents", "Resources", "inspector", ".h…
66 excludedFiles[filepath.Join(outputDir, "resources", "inspector", ".htaccess")] = true
68 excludedFiles[filepath.Join(outputDir, "version")] = true
71 err = zipx.Unzip(zipFile, outputDir, excludedFiles)
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/dports/devel/pear-PHP_UML/PHP_UML-1.6.2/UML/Output/
H A DExporterXSL.php71 * @param string $outputDir Output directory
80 return $this->transform($outputDir, $xslFile, $xmlDom);
91 * @param string $outputDir Output directory
103 return $this->transform($outputDir, $xslFile, $xmlDom);
117 * @param string $outputDir Output folder
121 public function export($outputDir) argument
155 * @param string $outputDir Output folder
180 if ($outputDir=='')
184 if (!file_exists($outputDir))
186 'Directory '.$outputDir.' does not exist.'
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/dports/net-p2p/vuze/vuze-5.7.4.0_2/org/gudy/azureus2/ui/console/commands/
H A DAddFind.java70 String outputDir = "."; in execute() local
72 outputDir = commands.getOptionValue('o'); in execute()
74 outputDir = ci.getDefaultSaveDirectory(); in execute()
76 File f = new File(outputDir); in execute()
81 outputDir = new File(".", outputDir).getCanonicalPath(); in execute()
95 addRemote(ci, arg, outputDir); in execute()
114 ci.downloadRemoteTorrent(arg, outputDir); in addRemote()
139 addFiles( ci, toadd, finding, outputDir ); in addLocal()
145 ci.downloadTorrent(arg, outputDir); in addLocal()
158 ci.downloadTorrent(torrentPath, outputDir); in addLocal()
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/dports/sysutils/istio/istio-1.6.7/vendor/github.com/antlr/antlr4/tool/src/org/antlr/v4/tool/
H A DBuildDependencyGenerator.java162 File outputDir = tool.getOutputDirectory(g.fileName); in getOutputFile() local
163 if ( outputDir.toString().equals(".") ) { in getOutputFile()
165 outputDir = tool.getOutputDirectory(fileName); in getOutputFile()
167 if ( outputDir.toString().equals(".") ) { in getOutputFile()
170 if (outputDir.getName().equals(".")) { in getOutputFile()
171 String fname = outputDir.toString(); in getOutputFile()
173 outputDir = new File(outputDir.toString().substring(0,dot)); in getOutputFile()
178 outputDir = new File(escSpaces); in getOutputFile()
180 return new File(outputDir, fileName); in getOutputFile()
256 if (outputDir.equals(".")) { in groomQualifiedFileName()
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/dports/biology/checkm/CheckM-1.0.18/scripts/genometreeworkflow/
H A DcreateSmallTree.py43 def __init__(self, outputDir): argument
47 self.tree = os.path.join(outputDir, 'genome_tree.final.tre')
77 def __nearlyIdenticalGenomes(self, seqs, outputDir): argument
81 nearlyIdenticalFile = os.path.join(outputDir, 'nearly_identical.tsv')
136 def run(self, outputDir): argument
138 if not os.path.exists(outputDir):
139 os.mkdir(outputDir)
145 nearlyIdentical = self.__nearlyIdenticalGenomes(seqs, outputDir)
153 reducedAlignmentFile = os.path.join(outputDir, "genome_tree.fasta")
168 outputTree = os.path.join(outputDir, 'genome_tree.tre')
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/dports/devel/spark/spark-2.1.1/core/src/test/scala/org/apache/spark/
H A DFileSuite.scala58 nums.saveAsTextFile(outputDir)
92 nums.saveAsSequenceFile(outputDir)
123 nums.saveAsSequenceFile(outputDir)
133 nums.saveAsSequenceFile(outputDir)
143 nums.saveAsSequenceFile(outputDir)
153 nums.saveAsSequenceFile(outputDir)
169 nums.saveAsObjectFile(outputDir)
179 nums.saveAsObjectFile(outputDir)
199 objs.saveAsObjectFile(outputDir)
218 outputDir)
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/dports/biology/mothur/mothur-1.46.1/source/read/
H A Dsplitmatrix.cpp29 outputDir = output; in SplitMatrix()
92 string thisOutputDir = outputDir; in createDistanceFilesFromTax()
123 thisOutputDir = outputDir; in createDistanceFilesFromTax()
130 thisOutputDir = outputDir; in createDistanceFilesFromTax()
140 thisOutputDir = outputDir; in createDistanceFilesFromTax()
169 thisOutputDir = outputDir; in createDistanceFilesFromTax()
204 thisOutputDir = outputDir; in createDistanceFilesFromTax()
211 thisOutputDir = outputDir; in createDistanceFilesFromTax()
246 string thisOutputDir = outputDir; in createFastaFilesFromTax()
280 thisOutputDir = outputDir; in createFastaFilesFromTax()
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/dports/java/openjdk11/jdk11u-jdk-11.0.13-8-1/src/jdk.rmic/share/classes/sun/rmi/rmic/
H A DUtil.java62 File outputDir = null; in getOutputDirectoryFor() local
83 outputDir = new File(rootDir, packagePath); in getOutputDirectoryFor()
87 ensureDirectory(outputDir,env); in getOutputDirectoryFor()
93 outputDir = rootDir; in getOutputDirectoryFor()
108 outputDir = workingDir; in getOutputDirectoryFor()
114 outputDir = new File(workingDir, packagePath); in getOutputDirectoryFor()
118 ensureDirectory(outputDir,env); in getOutputDirectoryFor()
124 return outputDir; in getOutputDirectoryFor()
/dports/java/openjdk13/jdk13u-jdk-13.0.10-1-1/src/jdk.rmic/share/classes/sun/rmi/rmic/
H A DUtil.java62 File outputDir = null; in getOutputDirectoryFor() local
83 outputDir = new File(rootDir, packagePath); in getOutputDirectoryFor()
87 ensureDirectory(outputDir,env); in getOutputDirectoryFor()
93 outputDir = rootDir; in getOutputDirectoryFor()
108 outputDir = workingDir; in getOutputDirectoryFor()
114 outputDir = new File(workingDir, packagePath); in getOutputDirectoryFor()
118 ensureDirectory(outputDir,env); in getOutputDirectoryFor()
124 return outputDir; in getOutputDirectoryFor()
/dports/java/openjdk8/jdk8u-jdk8u312-b07.1/jdk/src/share/classes/sun/rmi/rmic/
H A DUtil.java62 File outputDir = null; in getOutputDirectoryFor() local
83 outputDir = new File(rootDir, packagePath); in getOutputDirectoryFor()
87 ensureDirectory(outputDir,env); in getOutputDirectoryFor()
93 outputDir = rootDir; in getOutputDirectoryFor()
108 outputDir = workingDir; in getOutputDirectoryFor()
114 outputDir = new File(workingDir, packagePath); in getOutputDirectoryFor()
118 ensureDirectory(outputDir,env); in getOutputDirectoryFor()
124 return outputDir; in getOutputDirectoryFor()
/dports/java/openjdk11-jre/jdk11u-jdk-11.0.13-8-1/src/jdk.rmic/share/classes/sun/rmi/rmic/
H A DUtil.java62 File outputDir = null; in getOutputDirectoryFor() local
83 outputDir = new File(rootDir, packagePath); in getOutputDirectoryFor()
87 ensureDirectory(outputDir,env); in getOutputDirectoryFor()
93 outputDir = rootDir; in getOutputDirectoryFor()
108 outputDir = workingDir; in getOutputDirectoryFor()
114 outputDir = new File(workingDir, packagePath); in getOutputDirectoryFor()
118 ensureDirectory(outputDir,env); in getOutputDirectoryFor()
124 return outputDir; in getOutputDirectoryFor()
/dports/java/openjdk12/openjdk-jdk12u-jdk-12.0.2-10-4/src/jdk.rmic/share/classes/sun/rmi/rmic/
H A DUtil.java62 File outputDir = null; in getOutputDirectoryFor() local
83 outputDir = new File(rootDir, packagePath); in getOutputDirectoryFor()
87 ensureDirectory(outputDir,env); in getOutputDirectoryFor()
93 outputDir = rootDir; in getOutputDirectoryFor()
108 outputDir = workingDir; in getOutputDirectoryFor()
114 outputDir = new File(workingDir, packagePath); in getOutputDirectoryFor()
118 ensureDirectory(outputDir,env); in getOutputDirectoryFor()
124 return outputDir; in getOutputDirectoryFor()

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