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Searched refs:summaryFile (Results 1 – 25 of 63) sorted by relevance

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/dports/biology/bedtools/bedtools2-2.30.0/src/summaryFile/
H A DMakefile.frag1 BUILT_OBJECTS += obj/summaryHelp.o obj/summaryFile.o
3 obj/summaryHelp.o: src/summaryFile/summaryHelp.cpp obj/summaryHelp.d
6 obj/summaryFile.o: src/summaryFile/summaryFile.cpp obj/summaryFile.d
/dports/graphics/opencollada/OpenCOLLADA-1.6.68/xsd2cppsax/src/de/netallied/xsd2cppsax/testsuite/
H A DTestSuite.java89 private PrintStream summaryFile; field in TestSuite
149 summaryFile.println(new Date(System.currentTimeMillis()).toString() + " " + msg); in logToSummary()
200 summaryFile = new PrintStream(outDir + "/" + SUMMARY_FILE_NAME); in run()
204 summaryFile.println(); in run()
252 if (summaryFile != null) { in run()
253 summaryFile.close(); in run()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/validation/basicshortmutpileup/
H A DValidateBasicSomaticShortMutationsIntegrationTest.java32 final File summaryFile = IOUtils.createTempFile("summary", ".txt"); in testBasic() local
59 arguments.add(summaryFile.getAbsolutePath()); in testBasic()
67 Assert.assertTrue(summaryFile.exists()); in testBasic()
98 final File summaryFile = IOUtils.createTempFile("summary", ".txt"); in testIndelCase() local
127 arguments.add(summaryFile.getAbsolutePath()); in testIndelCase()
134 Assert.assertTrue(summaryFile.exists()); in testIndelCase()
/dports/print/lyx/lyx-2.3.4.2/development/checkurls/
H A Dsearch_url.pl63 my $summaryFile = undef;
97 $summaryFile = $val;
184 if (defined($summaryFile)) {
194 if ($outSum && defined($summaryFile)) {
/dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.platform.runtime/tests/org.eclipse.core.tests.harness/src/org/eclipse/core/tests/harness/
H A DFileSystemComparator.java110 File summaryFile = new File(rootLocation, SNAPSHOT_FILE_NAME); in loadSnapshot() local
112 …try (BufferedReader in = new BufferedReader(new InputStreamReader(new FileInputStream(summaryFile)… in loadSnapshot()
125 File summaryFile = new File(rootLocation, SNAPSHOT_FILE_NAME); in saveSnapshot() local
126 …w PrintWriter(new OutputStreamWriter(new BufferedOutputStream(new FileOutputStream(summaryFile)))); in saveSnapshot()
/dports/biology/mothur/mothur-1.46.1/source/commands/
H A Dsummarytaxcommand.cpp226 string summaryFile = getOutputFileName("summary",variables); in execute() local
227 util.openOutputFile(summaryFile, outTaxTree); in execute()
234 if (m->getControl_pressed()) { util.mothurRemove(summaryFile); return 0; } in execute()
239 …m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes[… in execute()
H A Dlibshuffcommand.cpp299 summaryFile = getOutputFileName("coverage", variables); in printCoverageFile()
300 util.openOutputFile(summaryFile, outCov); in printCoverageFile()
301 outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile); in printCoverageFile()
394 summaryFile = getOutputFileName("libshuffsummary",variables); in printSummaryFile()
395 util.openOutputFile(summaryFile, outSum); in printSummaryFile()
396 outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile); in printSummaryFile()
H A Dsummaryqualcommand.cpp151 string summaryFile = getOutputFileName("summary",variables); in execute() local
152 printQual(summaryFile, position, averageQ, scores); in execute()
154 if (m->getControl_pressed()) { util.mothurRemove(summaryFile); return 0; } in execute()
165 outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile); in execute()
168 m->mothurOut(summaryFile+"\n\n"); in execute()
H A Dgetmetacommunitycommand.cpp604 ofstream summaryFile; in generateSummaryFile() local
605 util.openOutputFile(summaryFileName, summaryFile); //((fileRoot + "mix.summary").c_str()); in generateSummaryFile()
606 summaryFile.setf(ios::fixed, ios::floatfield); in generateSummaryFile()
607 summaryFile.setf(ios::showpoint); in generateSummaryFile()
610 summaryFile << "OTU\tP0.mean"; in generateSummaryFile()
612 summaryFile << "\tP" << i+1 << ".mean\tP" << i+1 << ".lci\tP" << i+1 << ".uci"; in generateSummaryFile()
614 summaryFile << "\tDifference\tCumFraction" << endl; in generateSummaryFile()
620 summaryFile << summary[i].name << setprecision(2) << '\t' << summary[i].refMean; in generateSummaryFile()
622 …summaryFile << '\t' << summary[i].partMean[j] << '\t' << summary[i].partLCI[j] << '\t' << summary… in generateSummaryFile()
626 summaryFile << '\t' << summary[i].difference << '\t' << cumDiff << endl; in generateSummaryFile()
[all …]
H A Dlibshuffcommand.h47 string coverageFile, summaryFile, phylipfile, groupfile; variable
/dports/devel/hadoop2/hadoop-2.7.2-src/hadoop-mapreduce-project/hadoop-mapreduce-client/hadoop-mapreduce-client-hs/src/test/java/org/apache/hadoop/mapreduce/v2/hs/
H A DTestHistoryFileManager.java233 Path summaryFile = new Path(job + ".summary"); in testHistoryFileInfoSummaryFileNotExist() local
243 summaryFile, jobIndexInfo, false); in testHistoryFileInfoSummaryFileNotExist()
253 Path confFile, Path summaryFile, JobIndexInfo jobIndexInfo, in getHistoryFileInfo() argument
255 return new HistoryFileInfo(historyFile, confFile, summaryFile, in getHistoryFileInfo()
/dports/devel/hadoop2/hadoop-2.7.2-src/hadoop-mapreduce-project/hadoop-mapreduce-client/hadoop-mapreduce-client-hs/src/main/java/org/apache/hadoop/mapreduce/v2/hs/
H A DHistoryFileManager.java302 private Path summaryFile; field in HistoryFileManager.HistoryFileInfo
308 Path summaryFile, JobIndexInfo jobIndexInfo, boolean isInDone) { in HistoryFileInfo() argument
311 this.summaryFile = summaryFile; in HistoryFileInfo()
373 if (summaryFile == null || !intermediateDoneDirFc.util().exists( in moveToDone()
374 summaryFile)) { in moveToDone()
378 summaryFile); in moveToDone()
380 LOG.info("Deleting JobSummary file: [" + summaryFile + "]"); in moveToDone()
381 intermediateDoneDirFc.delete(summaryFile, false); in moveToDone()
382 summaryFile = null; in moveToDone()
/dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.platform.releng.tychoeclipsebuilder/eclipse/publishingFiles/templateFiles/
H A Dindex.template_java15.php136 $summaryFile=glob("buildFailed-*"); variable
140 echo "or a <a href=\"$summaryFile[0]\">summary</a>. <br /> \n";
H A Dindex.template_master.php141 $summaryFile=glob("buildFailed-*"); variable
145 echo "or a <a href=\"$summaryFile[0]\">summary</a>. <br /> \n";
/dports/biology/checkm/CheckM-1.0.18/checkm/
H A DssuFinder.py234 summaryFile = os.path.join(outputDir, 'ssu_summary.tsv')
235 summaryOut = open(summaryFile, 'w')
272 self.logger.info('Summary of identified hits written to: ' + summaryFile)
/dports/biology/mothur/mothur-1.46.1/source/
H A Dsummary.hpp124 string filename, summaryFile, contigsfile, output; member
146 summaryFile = sum; in seqSumData()
/dports/java/berkeley-db/je-6.2.31/test/com/sleepycat/je/logversion/
H A DMakeLogEntryVersionData.java86 File summaryFile = new File(homeDir, "je-" + in main() local
272 (new BufferedOutputStream(new FileOutputStream(summaryFile))); in main()
298 System.out.println("Created: " + summaryFile); in main()
/dports/math/g2o/g2o-20201223_git/g2o/apps/g2o_hierarchical/
H A Dg2o_hierarchical.cpp129 string summaryFile; in main() local
159 …arg.param("summary", summaryFile, "", "append a summary of this optimization run to the summary fi… in main()
532 if (summaryFile!="") { in main()
581 os.open(summaryFile.c_str(), ios::app); in main()
/dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.jdt.core/org.eclipse.jdt.apt.pluggable.tests/src/org/eclipse/jdt/apt/pluggable/tests/processors/genclass6/
H A DGenClass6Proc.java206 …FileObject summaryFile = _filer.createResource(StandardLocation.SOURCE_OUTPUT, "", "summary.txt", … in summarize() local
207 pw = new PrintWriter(summaryFile.openWriter()); in summarize()
/dports/math/g2o/g2o-20201223_git/g2o/apps/g2o_cli/
H A Dg2o.cpp131 string summaryFile; in main() local
166 …arg.param("summary", summaryFile, "", "append a summary of this optimization run to the summary fi… in main()
613 if (summaryFile!="") { in main()
649 os.open(summaryFile.c_str(), ios::app); in main()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/dragstr/
H A DSTRTableFileBuilder.java161 final File summaryFile = new File(dir, STRTableFile.SUMMARY_FILE_NAME); in writeSummary() local
162 try (final PrintWriter writer = new PrintWriter(new FileWriter(summaryFile))) { in writeSummary()
/dports/mail/thunderbird/thunderbird-91.8.0/comm/mailnews/local/src/
H A DnsMsgBrkMBoxStore.cpp398 nsCOMPtr<nsIFile> summaryFile; in CopyFolder() local
399 GetSummaryFileLocation(oldPath, getter_AddRefs(summaryFile)); in CopyFolder()
428 rv = summaryFile->CopyTo(newPath, dbName); in CopyFolder()
434 summaryFile->Exists(&exists); in CopyFolder()
435 summaryFile->GetFileSize(&fileSize); in CopyFolder()
H A DnsMsgMaildirStore.cpp421 nsCOMPtr<nsIFile> summaryFile; in CopyFolder() local
422 GetSummaryFileLocation(oldPath, getter_AddRefs(summaryFile)); in CopyFolder()
446 rv = summaryFile->CopyTo(newPath, dbName); in CopyFolder()
451 summaryFile->Exists(&exists); in CopyFolder()
452 summaryFile->GetFileSize(&fileSize); in CopyFolder()
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/
H A Dquerystatus.py390 summaryFile = '%s%s%s/%s%s' % (INSTALLDIR, TMPDIR, jobid, jobid, ".summary")
391 if os.path.isfile(summaryFile):
392 with open(summaryFile) as f:
/dports/sysutils/helmfile/helmfile-0.138.7/vendor/golang.org/x/tools/internal/lsp/tests/
H A Dtests.go41 summaryFile = "summary.txt" const
310 summary := filepath.Join(filepath.FromSlash(dir), summaryFile+goldenFileSuffix)
318 datum.golden[summaryFile] = &Golden{
379 if k == summaryFile {
895 want := string(data.Golden("summary", summaryFile, func() ([]byte, error) {
938 if fragment != summaryFile {

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