| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/copynumber/ |
| H A D | ModelSegmentsIntegrationTest.java | 45 final String outputPrefix = "test"; in testAllInputsAvailable() local
59 final String outputPrefix = "test"; in testNoNormalAllelicCounts() local
72 final String outputPrefix = "test"; in testNoDenoisedCopyRatios() local
85 final String outputPrefix = "test"; in testAllelicCountsOnly() local
97 final String outputPrefix = "test"; in testNoAllelicCounts() local
156 final String outputPrefix = "test"; in testSampleNameMismatch() local
169 final String outputPrefix = "test"; in testMissingSites() local
181 final String outputPrefix = "test"; in testNonExistentDenoisedCopyRatiosFile() local
194 final String outputPrefix = "test"; in testNonExistentAllelicCountsFile() local
207 final String outputPrefix = "test"; in testNonExistentNormalAllelicCountsFile() local
[all …]
|
| /dports/cad/fritzing/fritzing-parts-0.9.2b/parts/part-gen-scripts/misc_scripts/ |
| H A D | fzpzclean.py | 35 outputPrefix = None
46 outputPrefix = a
59 if(not(outputPrefix)):
77 createstructure(file, outputdir, outputPrefix)
100 subdir = outputPrefix
102 subdir = 'svg/' + outputPrefix + '/icon'
104 subdir = 'svg/' + outputPrefix + '/pcb'
106 subdir = 'svg/' + outputPrefix + '/schematic'
108 subdir = 'svg/' + outputPrefix + '/breadboard'
157 def createstructure(file, dir, outputPrefix): argument
[all …]
|
| /dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/SuperReadsR/src2/ |
| H A D | getLengthStatisticsForKUnitigsFile.perl | 20 $outputPrefix = "";
25 $outputPrefix = $ARGV[$i];
26 if ($outputPrefix !~ /\.$/) { $outputPrefix .= "."; }
31 $numKUnitigsFile = $outputPrefix . "numKUnitigs.txt";
32 $maxKUnitigNumberFile = $outputPrefix . "maxKUnitigNumber.txt";
33 $totBasesInKUnitigsFile = $outputPrefix . "totBasesInKUnitigs.txt";
|
| /dports/biology/star/STAR-2.7.9a/source/ |
| H A D | SoloFeature_processRecords.cpp | 16 outputPrefix= P.outFileNamePrefix+pSolo.outFileNames[0]; in processRecords()
17 outputPrefix+= SoloFeatureTypes::Names[featureType] +'/'; in processRecords()
18 outputPrefixFiltered= outputPrefix + "filtered/"; in processRecords()
20 if (mkdir(outputPrefix.c_str(),P.runDirPerm)!=0 && errno!=EEXIST) {//create directory in processRecords()
22 …NG because of fatal OUTPUT FILE error: could not create Solo output directory"<<outputPrefix<<"\n"; in processRecords()
61 ofstream *statsStream = &ofstrOpen(outputPrefix+"Features.stats",ERROR_OUT, P); in processRecords()
69 outputResults(false, outputPrefix + "/raw/"); //unfiltered in processRecords()
|
| /dports/biology/canu/canu-2.2/src/overlapBasedTrimming/ |
| H A D | trimStat.H | 42 void generatePlots(char const *outputPrefix, char const *outputName, uint32 binwidth) { in generatePlots() argument
46 snprintf(N, FILENAME_MAX, "%s.%s.dat", outputPrefix, outputName); in generatePlots()
52 snprintf(N, FILENAME_MAX, "%s.%s.gp", outputPrefix, outputName); in generatePlots()
63 fprintf(F, "set output '%s.%s.png'\n", outputPrefix, outputName); in generatePlots()
64 ….dat' using (bin($1,binwidth)):(1.0) smooth freq with boxes title ''\n", outputPrefix, outputName); in generatePlots()
67 snprintf(N, FILENAME_MAX, "gnuplot %s.%s.gp > /dev/null 2>&1", outputPrefix, outputName); in generatePlots()
|
| H A D | trimReads.C | 104 char *outputPrefix = NULL; in main() local
166 outputPrefix = argv[++arg]; in main()
181 (outputPrefix == NULL) || in main()
226 if (outputPrefix) { in main()
227 snprintf(logName, FILENAME_MAX, "%s.log", outputPrefix); in main()
445 if (outputPrefix) { in main()
446 snprintf(sumName, FILENAME_MAX, "%s.stats", outputPrefix); in main()
468 readsIn .generatePlots(outputPrefix, "inputReads", 250); in main()
469 deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250); in main()
491 trim5.generatePlots(outputPrefix, "trim5", 25); in main()
[all …]
|
| /dports/textproc/miller/miller-5.10.2/go/src/transformers/ |
| H A D | histogram.go | 66 outputPrefix := ""
94 outputPrefix = cliutil.VerbGetStringArgOrDie(verb, opt, args, &argi, argc)
119 outputPrefix,
138 outputPrefix string member
150 outputPrefix string,
164 outputPrefix: outputPrefix,
239 countFieldNames[valueFieldName] = this.outputPrefix + valueFieldName + "_count"
245 this.outputPrefix+"bin_lo",
249 this.outputPrefix+"bin_hi",
349 this.outputPrefix+"bin_lo",
[all …]
|
| /dports/games/powder-toy/The-Powder-Toy-95.0/src/ |
| H A D | PowderToyRenderer.cpp | 62 ByteString outputPrefix, inputFilename; in main() local
68 outputPrefix = argv[2]; in main()
70 ppmFilename = outputPrefix+".ppm"; in main()
71 ptiFilename = outputPrefix+".pti"; in main()
72 ptiSmallFilename = outputPrefix+"-small.pti"; in main()
73 pngFilename = outputPrefix+".png"; in main()
74 pngSmallFilename = outputPrefix+"-small.png"; in main()
|
| /dports/science/InsightToolkit/ITK-5.0.1/Examples/Filtering/ |
| H A D | SecondDerivativeRecursiveGaussianImageFilter.cxx | 108 std::string outputPrefix = argv[2]; in main() local
181 outputFileName = outputPrefix + "-Izz.mhd"; in main()
208 outputFileName = outputPrefix + "-Iyy.mhd"; in main()
230 outputFileName = outputPrefix + "-Ixx.mhd"; in main()
259 outputFileName = outputPrefix + "-Iyz.mhd"; in main()
293 outputFileName = outputPrefix + "-Ixz.mhd"; in main()
311 outputFileName = outputPrefix + "-Ixy.mhd"; in main()
|
| /dports/graphics/libpano13/libpano13-2.9.20/tools/ |
| H A D | PTmasker.c | 93 char outputPrefix[MAX_PATH_LENGTH]; in main() local
105 outputPrefix[0] = 0; in main()
149 strcpy(outputPrefix, optarg); in main()
180 if (!(*outputPrefix)) { in main()
181 strcpy(outputPrefix, "masked"); in main()
242 if (panoFileOutputNamesCreate(ptrOutputFiles, filesCount, outputPrefix) == 0) { in main()
|
| H A D | PTblender.c | 81 char outputPrefix[MAX_PATH_LENGTH]; in main() local
96 strcpy(outputPrefix, DEFAULT_PREFIX); in main()
108 strcpy(outputPrefix, optarg); in main()
198 if (panoFileOutputNamesCreate(ptrOutputFiles, filesCount, outputPrefix) == 0) { in main()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/ |
| H A D | SvDiscoverFromLocalAssemblyContigAlignmentsSpark.java | 115 private String outputPrefix; field in SvDiscoverFromLocalAssemblyContigAlignmentsSpark
183 if ( Files.exists(Paths.get(outputPrefix)) ) { in getOutputPrefix()
184 if (Files.isDirectory(Paths.get(outputPrefix))) // existing directory in getOutputPrefix()
185 …return outputPrefix + (outputPrefix.endsWith("/") ? "" : "/") + SVUtils.getSampleId(getHeaderForRe… in getOutputPrefix()
187 …tion("Provided prefix for output is pointing to an existing file: " + outputPrefix); // to avoid a… in getOutputPrefix()
189 …return outputPrefix + (outputPrefix.endsWith("/") ? "" : "_") + SVUtils.getSampleId(getHeaderForRe… in getOutputPrefix()
228 …private void writeSAMfilesForUnknown(final String outputPrefix, final JavaRDD<GATKRead> assemblyRa… in writeSAMfilesForUnknown() argument
245 …factory.makeSAMOrBAMWriter(clone, true, IOUtils.getPath(outputPrefix + ReasonForAlignmentClassific… in writeSAMfilesForUnknown()
248 …factory.makeSAMOrBAMWriter(clone, true, IOUtils.getPath(outputPrefix + ReasonForAlignmentClassific… in writeSAMfilesForUnknown()
251 …factory.makeSAMOrBAMWriter(clone, true, IOUtils.getPath(outputPrefix + ReasonForAlignmentClassific… in writeSAMfilesForUnknown()
|
| /dports/graphics/hugin/hugin-2020.0.0/src/hugin1/executor/ |
| H A D | hugin_executor.cpp | 143 wxFileName outputPrefix; in OnRun() local
146 outputPrefix = getDefaultOutputName(m_input, pano); in OnRun()
147 outputPrefix.Normalize(); in OnRun()
151 outputPrefix = m_prefix; in OnRun()
152 outputPrefix.MakeAbsolute(); in OnRun()
155 wxFileName::SetCwd(outputPrefix.GetPath()); in OnRun()
160 …etStitchingCommandQueue(pano, m_utilsBinDir, inputFile.GetFullPath(), outputPrefix.GetName(), stat… in OnRun()
164 …gCommandQueueUserOutput(pano, m_utilsBinDir, inputFile.GetFullPath(), outputPrefix.GetName(), m_us… in OnRun()
|
| /dports/java/openjdk11/jdk11u-jdk-11.0.13-8-1/test/hotspot/jtreg/vmTestbase/nsk/share/aod/ |
| H A D | ProcessExecutor.java | 56 private String outputPrefix; field in ProcessExecutor.InputStreamReaderThread
66 this.outputPrefix = prefix; in InputStreamReaderThread()
84 System.out.println(outputPrefix + line); in run()
155 public ProcessExecutor(String cmdLine, long timeout, String outputPrefix) { in ProcessExecutor() argument
158 this.processOutputPrefix = outputPrefix; in ProcessExecutor()
|
| /dports/java/openjdk12/openjdk-jdk12u-jdk-12.0.2-10-4/test/hotspot/jtreg/vmTestbase/nsk/share/aod/ |
| H A D | ProcessExecutor.java | 56 private String outputPrefix; field in ProcessExecutor.InputStreamReaderThread
66 this.outputPrefix = prefix; in InputStreamReaderThread()
84 System.out.println(outputPrefix + line); in run()
155 public ProcessExecutor(String cmdLine, long timeout, String outputPrefix) { in ProcessExecutor() argument
158 this.processOutputPrefix = outputPrefix; in ProcessExecutor()
|
| /dports/java/openjdk13/jdk13u-jdk-13.0.10-1-1/test/hotspot/jtreg/vmTestbase/nsk/share/aod/ |
| H A D | ProcessExecutor.java | 56 private String outputPrefix; field in ProcessExecutor.InputStreamReaderThread
66 this.outputPrefix = prefix; in InputStreamReaderThread()
84 System.out.println(outputPrefix + line); in run()
155 public ProcessExecutor(String cmdLine, long timeout, String outputPrefix) { in ProcessExecutor() argument
158 this.processOutputPrefix = outputPrefix; in ProcessExecutor()
|
| /dports/java/openjdk15/jdk15u-jdk-15.0.6-1-1/test/hotspot/jtreg/vmTestbase/nsk/share/aod/ |
| H A D | ProcessExecutor.java | 56 private String outputPrefix; field in ProcessExecutor.InputStreamReaderThread
66 this.outputPrefix = prefix; in InputStreamReaderThread()
84 System.out.println(outputPrefix + line); in run()
155 public ProcessExecutor(String cmdLine, long timeout, String outputPrefix) { in ProcessExecutor() argument
158 this.processOutputPrefix = outputPrefix; in ProcessExecutor()
|
| /dports/java/openjdk16/jdk16u-jdk-16.0.2-7-1/test/hotspot/jtreg/vmTestbase/nsk/share/aod/ |
| H A D | ProcessExecutor.java | 56 private String outputPrefix; in targetApplicationActions()
66 this.outputPrefix = prefix; in targetApplicationActions()
84 System.out.println(outputPrefix + line); in targetApplicationActions()
155 public ProcessExecutor(String cmdLine, long timeout, String outputPrefix) {
158 this.processOutputPrefix = outputPrefix;
|
| /dports/java/openjdk17/jdk17u-jdk-17.0.1-12-1/test/hotspot/jtreg/vmTestbase/nsk/share/aod/ |
| H A D | ProcessExecutor.java | 56 private String outputPrefix; field in ProcessExecutor.InputStreamReaderThread
66 this.outputPrefix = prefix; in InputStreamReaderThread()
84 System.out.println(outputPrefix + line); in run()
155 public ProcessExecutor(String cmdLine, long timeout, String outputPrefix) { in ProcessExecutor() argument
158 this.processOutputPrefix = outputPrefix; in ProcessExecutor()
|
| /dports/java/openjdk11-jre/jdk11u-jdk-11.0.13-8-1/test/hotspot/jtreg/vmTestbase/nsk/share/aod/ |
| H A D | ProcessExecutor.java | 56 private String outputPrefix; field in ProcessExecutor.InputStreamReaderThread
66 this.outputPrefix = prefix; in InputStreamReaderThread()
84 System.out.println(outputPrefix + line); in run()
155 public ProcessExecutor(String cmdLine, long timeout, String outputPrefix) { in ProcessExecutor() argument
158 this.processOutputPrefix = outputPrefix; in ProcessExecutor()
|
| /dports/java/openjdk14/jdk14u-jdk-14.0.2-12-1/test/hotspot/jtreg/vmTestbase/nsk/share/aod/ |
| H A D | ProcessExecutor.java | 56 private String outputPrefix; field in ProcessExecutor.InputStreamReaderThread
66 this.outputPrefix = prefix; in InputStreamReaderThread()
84 System.out.println(outputPrefix + line); in run()
155 public ProcessExecutor(String cmdLine, long timeout, String outputPrefix) { in ProcessExecutor() argument
158 this.processOutputPrefix = outputPrefix; in ProcessExecutor()
|
| /dports/biology/canu/canu-2.2/src/correction/ |
| H A D | falconsense.C | 41 void openAlignLogFiles(char const *outputPrefix);
42 void closeAlignLogFiles(char const *outputPrefix);
262 char const *outputPrefix = NULL; in main() local
297 outputPrefix = argv[++arg]; in main()
452 FILE *cnsFile = AS_UTL_openOutputFile(outputPrefix, '.', "cns", outputCNS); in main()
453 FILE *seqFile = AS_UTL_openOutputFile(outputPrefix, '.', "fastq", outputFASTQ); in main()
457 openAlignLogFiles(outputPrefix); in main()
719 AS_UTL_closeFile(batFile, outputPrefix, '.', "batches"); in main()
720 AS_UTL_closeFile(seqFile, outputPrefix, '.', "fastq"); in main()
721 AS_UTL_closeFile(cnsFile, outputPrefix, '.', "cns"); in main()
[all …]
|
| /dports/math/vtk9/VTK-9.1.0/Examples/IO/Cxx/ |
| H A D | objtovtp.cxx | 66 std::string outputPrefix = "o2v"; in main() local
67 outputPrefix += vtksys::SystemTools::GetFilenameWithoutLastExtension(filenameOBJ); in main()
69 exporter->SetFilePrefix(outputPrefix.c_str()); in main()
|
| /dports/math/vtk8/VTK-8.2.0/Examples/IO/Cxx/ |
| H A D | objtovtp.cxx | 66 std::string outputPrefix = "o2v"; in main() local
67 outputPrefix += vtksys::SystemTools::GetFilenameWithoutLastExtension(filenameOBJ); in main()
69 exporter->SetFilePrefix(outputPrefix.c_str()); in main()
|
| /dports/biology/checkm/CheckM-1.0.18/checkm/ |
| H A D | ssuFinder.py | 40 def __hmmSearch(self, seqFile, evalue, outputPrefix): argument
47 …oali --cpu ' + str(self.totalThreads) + ' -o ' + outputPrefix + '.bacteria.txt --tblout ' + output…
50 …oali --cpu ' + str(self.totalThreads) + ' -o ' + outputPrefix + '.archaea.txt --tblout ' + outputP…
53 …-noali --cpu ' + str(self.totalThreads) + ' -o ' + outputPrefix + '.euk.txt --tblout ' + outputPre…
|