| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_assembly/ |
| H A D | CoverageInfo.cpp | 34 CHECK(!coverageInfo.isEmpty(), ) in updateStats()
35 maxCoverage = minCoverage = coverageInfo[0]; in updateStats()
39 for (int regionIndex = 0; regionIndex < coverageInfo.size(); ++regionIndex) { in updateStats()
40 maxCoverage = std::max(maxCoverage, coverageInfo[regionIndex]); in updateStats()
41 minCoverage = std::min(maxCoverage, coverageInfo[regionIndex]); in updateStats()
42 sum += coverageInfo[regionIndex]; in updateStats()
44 averageCoverage = (double)sum / coverageInfo.size(); in updateStats()
73 result.coverageInfo.resize(settings.regions); in run()
87 result.coverageInfo[regionIndex] = coverageStat[regionIndex]; in run()
93 result.coverageInfo[regionIndex] = 0; in run()
[all …]
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| H A D | CoveredRegionsManager.cpp | 30 …::CoveredRegionsManager(const U2Region &visibleRegion_, const U2AssemblyCoverageStat &coverageInfo) in CoveredRegionsManager() argument
32 assert(!coverageInfo.empty()); in CoveredRegionsManager()
37 … double step = double(visibleRegion.length) / coverageInfo.size(); // precise length of the region in CoveredRegionsManager()
40 int regionsCount = coverageInfo.size(); in CoveredRegionsManager()
49 maxCoverage = qMax(maxCoverage, coverageInfo[i * regionsToJoin + j]); in CoveredRegionsManager()
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| H A D | AssemblyCoverageGraph.cpp | 85 const U2AssemblyCoverageStat &coverageInfo = ci.coverageInfo; in drawGraph() local
88 …SAFE_POINT(visibleBases == coverageInfo.size(), "in AssemblyCoverageGraph::drawGraph: incorrect co… in drawGraph()
94 int columnPixels = qint64(double(coverageInfo[ibase]) / readsPerYPixel + 0.5); in drawGraph()
95 double grayCoeffD = double(coverageInfo[ibase]) / maxCoverage; in drawGraph()
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| H A D | CoverageInfo.h | 40 return coverageInfo.empty(); in isEmpty()
46 U2AssemblyCoverageStat coverageInfo; member
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| H A D | AssemblyBrowser.cpp | 354 if (newInfo.coverageInfo.size() <= coveredRegionsManager.getSize()) { in setGlobalCoverageInfo()
364 if (!status.isCoR() && coverageStat.size() > newInfo.coverageInfo.size()) { in setGlobalCoverageInfo()
365 newInfo.coverageInfo = coverageStat; in setGlobalCoverageInfo()
369 coveredRegionsManager = CoveredRegionsManager(globalRegion, newInfo.coverageInfo); in setGlobalCoverageInfo()
371 if (newInfo.coverageInfo.size() == newInfo.region.length) { in setGlobalCoverageInfo()
387 SAFE_POINT(coverage.region.length == coverage.coverageInfo.size(), in setLocalCoverageCache()
398 return localCoverageCache.coverageInfo.at(pos - localCoverageCache.region.startPos); in getCoverageAtPos()
423 ci.coverageInfo.resize(region.length); in extractFromLocalCoverageCache()
431 …y(ci.coverageInfo.data() + offsetInResult, localCoverageCache.coverageInfo.constData() + offsetInC… in extractFromLocalCoverageCache()
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| H A D | ZoomableAssemblyOverview.cpp | 197 if (!ci.coverageInfo.isEmpty()) { in drawBackground()
201 grayCoeffD = double(ci.coverageInfo[i]) / ci.maxCoverage; in drawBackground()
203 columnPixels = qint64(double(ci.coverageInfo[i]) / readsPerYPixel + 0.5); in drawBackground()
207 grayCoeffD = log((double)ci.coverageInfo[i]) / logMax; in drawBackground()
208 … columnPixels = qint64(double(log((double)ci.coverageInfo[i])) / readsPerYPixel + 0.5); in drawBackground()
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| /dports/graphics/ossim/ossim-OrchidIsland-2.11.1/src/imaging/ |
| H A D | ossimVpfAnnotationLibraryInfo.cpp | 164 ossimVpfAnnotationCoverageInfo* coverageInfo = in buildLibrary() local
166 coverageInfo->setName(coverageNames[idx]); in buildLibrary()
167 coverageInfo->setLibrary(library); in buildLibrary()
168 theCoverageLayerList.push_back(coverageInfo); in buildLibrary()
173 coverageInfo->buildCoverage(feature); in buildLibrary()
253 ossimVpfAnnotationCoverageInfo* coverageInfo = new ossimVpfAnnotationCoverageInfo; in loadState() local
254 coverageInfo->setLibrary(library); in loadState()
255 theCoverageLayerList.push_back(coverageInfo); in loadState()
256 coverageInfo->loadState(kwl, in loadState()
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| /dports/biology/checkm/CheckM-1.0.18/checkm/ |
| H A D | coverage.py | 80 coverageInfo = {}
86 coverageInfo[bamFile] = mp.Manager().dict()
87 …coverageInfo[bamFile] = self.__processBam(bamFile, bAllReads, minAlignPer, maxEditDistPer, minQC, …
100 for bamFile, seqIds in coverageInfo.iteritems():
110 if seqId in coverageInfo[bamFile]:
111 …rowStr += '\t%s\t%f\t%d' % (bamId, coverageInfo[bamFile][seqId].coverage, coverageInfo[bamFile][se…
120 def __processBam(self, bamFile, bAllReads, minAlignPer, maxEditDistPer, minQC, coverageInfo): argument
160 …writeProc = mp.Process(target=self.__writerThread, args=(coverageInfo, len(refSeqIds), writerQueue…
180 return coverageInfo
237 def __writerThread(self, coverageInfo, numRefSeqs, writerQueue): argument
[all …]
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| H A D | coverageWindows.py | 102 coverageInfo = mp.Manager().dict()
103 …coverageInfo = self.__processBam(bamFile, bAllReads, minAlignPer, maxEditDistPer, windowSize, cove…
105 return coverageInfo
107 … def __processBam(self, bamFile, bAllReads, minAlignPer, maxEditDistPer, windowSize, coverageInfo): argument
147 …writeProc = mp.Process(target=self.__writerThread, args=(coverageInfo, len(refSeqIds), writerQueue…
166 return coverageInfo
205 def __writerThread(self, coverageInfo, numRefSeqs, writerQueue): argument
237 coverageInfo[seqId] = [coverage, windowCoverages]
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| /dports/www/qt5-webengine/qtwebengine-everywhere-src-5.15.2/src/3rdparty/chromium/v8/src/builtins/ |
| H A D | internal-coverage.tq | 20 coverageInfo: CoverageInfo, slot: Smi) {
21 assert(Convert<int32>(slot) < coverageInfo.slot_count);
22 ++coverageInfo.slots[slot].block_count;
32 const coverageInfo: CoverageInfo =
34 IncrementBlockCount(coverageInfo, coverageArraySlotIndex);
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| /dports/lang/v8/v8-9.6.180.12/src/builtins/ |
| H A D | internal-coverage.tq | 20 coverageInfo: CoverageInfo, slot: Smi): void {
21 dcheck(Convert<int32>(slot) < coverageInfo.slot_count);
22 ++coverageInfo.slots[slot].block_count;
33 const coverageInfo: CoverageInfo =
35 IncrementBlockCount(coverageInfo, coverageArraySlotIndex);
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| /dports/www/chromium-legacy/chromium-88.0.4324.182/v8/src/builtins/ |
| H A D | internal-coverage.tq | 20 coverageInfo: CoverageInfo, slot: Smi) {
21 assert(Convert<int32>(slot) < coverageInfo.slot_count);
22 ++coverageInfo.slots[slot].block_count;
33 const coverageInfo: CoverageInfo =
35 IncrementBlockCount(coverageInfo, coverageArraySlotIndex);
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| /dports/www/orangehrm/orangehrm-4.9/symfony/lib/vendor/lexpress/doctrine1/tests/DoctrineTest/ |
| H A D | Coverage.php | 168 … $coverageInfo[$class] = $this->generateCoverageInfoCoveredFile($file->getPathname());
171 $coverageInfo[$class] = $this->generateCoverageInfoNotCoveredFile($class);
181 $this->result["data"] = $coverageInfo;
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| /dports/audio/rhvoice/RHVoice-1.2.4/src/third-party/cldr/tools/java/org/unicode/cldr/tool/ |
| H A D | ShowCoverageLevels.java | 28 CoverageInfo coverageInfo = CLDRConfig.getInstance().getCoverageInfo(); in main() local
38 Level level = coverageInfo.getCoverageLevel(fullPath, locale); in main()
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| H A D | ShowLocaleCoverage.java | 812 … Level level = coverageInfo.getCoverageLevel(mPath, locale); in showCoverage()
936 Level foundLevel = coverageInfo.getCoverageLevel(path, locale); in showCoverage()
943 Level foundLevel = coverageInfo.getCoverageLevel(path, locale); in showCoverage()
954 Level foundLevel = coverageInfo.getCoverageLevel(path, locale); in showCoverage()
960 Level foundLevel = coverageInfo.getCoverageLevel(path, locale); in showCoverage()
1099 Level foundLevel = coverageInfo.getCoverageLevel(path, locale); in showCoverage()
1248 static final CoverageInfo coverageInfo = new CoverageInfo(SUPPLEMENTAL_DATA_INFO); field in ShowLocaleCoverage
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| H A D | GenerateCoverageLevels.java | 552 CoverageInfo coverageInfo = CLDRConfig.getInstance().getCoverageInfo(); in Pseudolocalizer()
565 Level level = coverageInfo.getCoverageLevel(fullPath, locale); in Pseudolocalizer()
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| /dports/audio/rhvoice/RHVoice-1.2.4/src/third-party/cldr/tools/java/org/unicode/cldr/util/ |
| H A D | CLDRConfig.java | 155 private CoverageInfo coverageInfo = null; field in CLDRConfig
235 if (coverageInfo == null) { in getCoverageInfo()
236 coverageInfo = new CoverageInfo(getSupplementalDataInfo()); in getCoverageInfo()
239 return coverageInfo; in getCoverageInfo()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/dbi/ |
| H A D | U2AssemblyDbi.h | 75 U2AssemblyCoverageImportInfo coverageInfo; variable
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/util/ |
| H A D | MysqlMultiTableAssemblyAdapter.cpp | 256 rangeReadsImportInfo.coverageInfo = ii.coverageInfo; in addReads()
259 ii.coverageInfo = rangeReadsImportInfo.coverageInfo; in addReads()
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| H A D | MysqlSingleTableAssemblyAdapter.cpp | 216 MysqlAssemblyUtils::addToCoverage(ii.coverageInfo, read); in addReads()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/assembly/ |
| H A D | MultiTableAssemblyAdapter.cpp | 460 rangeReadsImportInfo.coverageInfo = ii.coverageInfo; in addReads()
463 ii.coverageInfo = rangeReadsImportInfo.coverageInfo; in addReads()
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| H A D | RTreeAssemblyAdapter.cpp | 171 SQLiteAssemblyUtils::addToCoverage(ii.coverageInfo, read); in addReads()
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| H A D | SingleTableAssemblyAdapter.cpp | 200 SQLiteAssemblyUtils::addToCoverage(ii.coverageInfo, read); in addReads()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/ace/ |
| H A D | ConvertAceToSqliteTask.cpp | 263 const U2AssemblyCoverageStat &coverageStat = importInfo.coverageInfo.coverage; in updateAttributeDbi()
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| /dports/biology/ugene/ugene-40.1/src/plugins/dbi_bam/src/ |
| H A D | ConvertToSQLiteTask.cpp | 613 enableCoverageOnImport(importInfo.coverageInfo, references[referenceId].getLength()); in importMappedSortedReads()
880 const U2AssemblyCoverageStat &coverageStat = importInfo.coverageInfo.coverage; in updateImportInfoCoverageStatAttribute()
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