/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/plotting/ |
H A D | PlotDenoisedCopyRatiosIntegrationTest.java | 33 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 [all …]
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H A D | PlotModeledSegmentsIntegrationTest.java | 41 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 [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/ |
H A D | SplitIntervalsIntegrationTest.java | 37 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() [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/ |
H A D | ModelSegmentsIntegrationTest.java | 50 .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() [all …]
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/dports/www/phalcon4/cphalcon-4.1.1/tests/unit/Image/Adapter/Gd/ |
H A D | WatermarkCest.php | 46 $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); [all …]
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H A D | CropCest.php | 40 $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)
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H A D | ResizeCest.php | 40 $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)
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/dports/devel/pear-phing/phing-2.6.1/tasks/ext/liquibase/ |
H A D | LiquibaseDbDocTask.php | 32 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));
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/dports/www/phalcon/cphalcon-3.4.5/build/_resource/Phalcon/Build/Generator/ |
H A D | Safe.php | 22 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) { [all …]
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/dports/www/phalcon4/cphalcon-4.1.1/build/_resource/Phalcon/Build/Generator/ |
H A D | Safe.php | 22 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 $line) { [all …]
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/dports/biology/checkm/CheckM-1.0.18/scripts/ |
H A D | genomeTreeWorkflow.py | 45 def __init__(self, outputDir): argument 47 if os.path.exists(outputDir): 48 print '[Error] Output directory already exists: ' + outputDir 51 os.makedirs(outputDir) 58 self.hmmDir = os.path.join(outputDir, 'phylo_hmms') 59 self.alignmentDir = os.path.join(outputDir, 'gene_alignments') 60 self.geneTreeDir = os.path.join(outputDir, 'gene_trees') 62 self.finalGeneTreeDir = os.path.join(outputDir, 'gene_trees_final') 63 self.bootstrapDir = os.path.join(outputDir, 'bootstrap') 68 self.treeOut = os.path.join(outputDir, 'genome_tree.tre') [all …]
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/dports/graphics/ossim/ossim-OrchidIsland-2.11.1/apps/ossim-applanix2ogeom/ |
H A D | ossim-applanix2ogeom.cpp | 40 const ossimFilename& outputDir); 122 ossimFilename outputDir; in main() local 131 if (outputDir.createDirectory() == false) in main() 140 outputDirOverrideFlag = outputDir.exists(); in main() 197 outputDir = imageToProcess.path(); in main() 199 processImage(eo, kwl, id, outputDir); in main() 206 if(!outputDir .isDir()) in main() 208 ossimFilename idFile = outputDir.file(); in main() 209 outputDir = outputDir.path(); in main() 301 if (outputDir != ossimFilename::NIL) in processImage() [all …]
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/dports/net/olsrd/olsrd-0.9.8/redhat/ |
H A D | runner | 22 outputDir="$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" [all …]
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/dports/devel/app-builder/app-builder-3.4.2/pkg/electron/ |
H A D | electronUnpack.go | 20 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) [all …]
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/dports/devel/pear-PHP_UML/PHP_UML-1.6.2/UML/Output/ |
H A D | ExporterXSL.php | 71 * @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.' [all …]
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/dports/net-p2p/vuze/vuze-5.7.4.0_2/org/gudy/azureus2/ui/console/commands/ |
H A D | AddFind.java | 70 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() [all …]
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/dports/sysutils/istio/istio-1.6.7/vendor/github.com/antlr/antlr4/tool/src/org/antlr/v4/tool/ |
H A D | BuildDependencyGenerator.java | 162 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() [all …]
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/dports/biology/checkm/CheckM-1.0.18/scripts/genometreeworkflow/ |
H A D | createSmallTree.py | 43 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') [all …]
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/dports/devel/spark/spark-2.1.1/core/src/test/scala/org/apache/spark/ |
H A D | FileSuite.scala | 58 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) [all …]
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/dports/biology/mothur/mothur-1.46.1/source/read/ |
H A D | splitmatrix.cpp | 29 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() [all …]
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/dports/java/openjdk11/jdk11u-jdk-11.0.13-8-1/src/jdk.rmic/share/classes/sun/rmi/rmic/ |
H A D | Util.java | 62 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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/dports/java/openjdk13/jdk13u-jdk-13.0.10-1-1/src/jdk.rmic/share/classes/sun/rmi/rmic/ |
H A D | Util.java | 62 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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/dports/java/openjdk8/jdk8u-jdk8u312-b07.1/jdk/src/share/classes/sun/rmi/rmic/ |
H A D | Util.java | 62 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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/dports/java/openjdk11-jre/jdk11u-jdk-11.0.13-8-1/src/jdk.rmic/share/classes/sun/rmi/rmic/ |
H A D | Util.java | 62 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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/dports/java/openjdk12/openjdk-jdk12u-jdk-12.0.2-10-4/src/jdk.rmic/share/classes/sun/rmi/rmic/ |
H A D | Util.java | 62 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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