| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/ |
| H A D | GATKReadFilterPluginDescriptor.java | 52 final GATKReadFilterArgumentCollection userArgs; field in GATKReadFilterPluginDescriptor
73 this.userArgs = userArgs; in GATKReadFilterPluginDescriptor()
203 userArgs.getDisableToolDefaultReadFilters() ? in getResolvedInstances()
224 userArgs.getUserEnabledReadFilterNames().forEach(s -> { in getUserEnabledInstances()
298 enabledAndDisabled.retainAll(userArgs.getUserDisabledReadFilterNames()); in validateAndResolvePlugins()
306 userArgs.getUserDisabledReadFilterNames().forEach(s -> { in validateAndResolvePlugins()
316 redundant.retainAll(userArgs.getUserEnabledReadFilterNames()); in validateAndResolvePlugins()
332 userArgs.getUserDisabledReadFilterNames().forEach(s -> { in validateAndResolvePlugins()
349 userArgs.getUserEnabledReadFilterNames().forEach(s -> { in validateAndResolvePlugins()
372 return userArgs.getUserDisabledReadFilterNames().contains(filterName) in isDisabledFilter()
[all …]
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| H A D | GATKAnnotationPluginDescriptor.java | 55 private final GATKAnnotationArgumentCollection userArgs; field in GATKAnnotationPluginDescriptor
113 this.userArgs = userArgs; in GATKAnnotationPluginDescriptor()
325 userArgs.getUserDisabledAnnotationNames().forEach(s -> { in validateAndResolvePlugins()
335 redundantAnnots.retainAll(userArgs.getUserEnabledAnnotationNames()); in validateAndResolvePlugins()
343 redundantGroups.retainAll(userArgs.getUserEnabledAnnotationGroups()); in validateAndResolvePlugins()
359 userArgs.getUserDisabledAnnotationNames().forEach(s -> { in validateAndResolvePlugins()
375 userArgs.getUserEnabledAnnotationNames().forEach(s -> { in validateAndResolvePlugins()
385 userArgs.getUserEnabledAnnotationGroups().forEach(s -> { in validateAndResolvePlugins()
449 if (!userArgs.getDisableToolDefaultAnnotations()) { in getResolvedInstances()
452 for (String group : userArgs.getUserEnabledAnnotationGroups()) { in getResolvedInstances()
[all …]
|
| /dports/devel/intel-graphics-compiler/intel-graphics-compiler-igc-1.0.9636/IGC/AdaptorOCL/ocl_igc_interface/impl/ |
| H A D | fcl_ocl_translation_ctx_impl.cpp | 199 llvm::SmallVectorImpl<const char*> &userArgs, in processCmSrcOptions() argument
203 auto toErase = std::find_if(userArgs.begin(), userArgs.end(), in processCmSrcOptions()
205 if (toErase != userArgs.end()) { in processCmSrcOptions()
209 userArgs.erase(toErase, toErase + 2); in processCmSrcOptions()
215 toErase = std::find_if(userArgs.begin(), userArgs.end(), in processCmSrcOptions()
220 if (toErase != userArgs.end()) { in processCmSrcOptions()
223 userArgs.erase(toErase); in processCmSrcOptions()
240 llvm::SmallVector<const char*, 20> userArgs; in processFeOptions() local
248 auto toErase = std::remove_if(userArgs.begin(), userArgs.end(), in processFeOptions()
250 userArgs.erase(toErase, userArgs.end()); in processFeOptions()
[all …]
|
| /dports/lang/mono/mono-5.10.1.57/mcs/class/referencesource/System/net/System/Net/Sockets/ |
| H A D | _MultipleConnectAsync.cs | 15 protected SocketAsyncEventArgs userArgs; field in System.Net.Sockets.MultipleConnectAsync
46 this.userArgs = args; in StartConnectAsync()
118 internalArgs.SetBuffer(userArgs.Buffer, userArgs.Offset, userArgs.Count); in DoDnsCallback()
258 …userArgs.FinishWrapperConnectSuccess(internalArgs.ConnectSocket, internalArgs.BytesTransferred, in… in Succeed()
289 userArgs.FinishConnectByNameSyncFailure(socketException, 0, SocketFlags.None); in SyncFail()
305 userArgs.FinishOperationAsyncFailure(e, 0, SocketFlags.None); in AsyncFail()
|
| /dports/devel/libqtxdg/libqtxdg-3.8.0/util/ |
| H A D | qtxdg-desktop-file-start.cpp | 51 QStringList userArgs = parser.positionalArguments(); in main() local
52 const QString userFileName = userArgs.takeFirst(); in main()
65 f.startDetached(userArgs); in main()
|
| /dports/lang/mono/mono-5.10.1.57/mcs/class/referencesource/System.Data.Linq/SqlClient/Reader/ |
| H A D | ObjectReader.cs | 33 … disposeReader, IReaderProvider provider, object[] parentArgs, object[] userArgs, ICompiledSubQuer… in Create() argument
39 …aReader reader, IReaderProvider provider, object[] parentArgs, object[] userArgs, ICompiledSubQuer… in CreateSession() argument
43 IExecuteResult Execute(IProvider provider, object[] parentArgs, object[] userArgs); in Execute() argument
|
| /dports/devel/kde-dev-scripts/kde-dev-scripts-21.12.3/ |
| H A D | unsercmake | 141 if($#userArgs >= 0) { # limit to user request
142 foreach $lib (@userArgs) {
145 if($#userArgs == 0) {
444 push @userArgs, $arguments[$i];
|
| /dports/databases/mariadb105-client/mariadb-10.5.15/storage/columnstore/columnstore/oamapps/postConfigure/ |
| H A D | mycnfUpgrade.cpp | 75 ifstream userArgs(userArgsFilename.c_str()); in mergeMycnfIncludeArgs() local
78 if (!userArgs || !packagedArgs) in mergeMycnfIncludeArgs()
92 while (getline(userArgs, line)) { in mergeMycnfIncludeArgs()
99 userArgs.close(); in mergeMycnfIncludeArgs()
|
| /dports/databases/mariadb105-server/mariadb-10.5.15/storage/columnstore/columnstore/oamapps/postConfigure/ |
| H A D | mycnfUpgrade.cpp | 75 ifstream userArgs(userArgsFilename.c_str()); in mergeMycnfIncludeArgs() local
78 if (!userArgs || !packagedArgs) in mergeMycnfIncludeArgs()
92 while (getline(userArgs, line)) { in mergeMycnfIncludeArgs()
99 userArgs.close(); in mergeMycnfIncludeArgs()
|
| /dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.pde.ui/ui/org.eclipse.pde.ui/src/org/eclipse/pde/internal/ui/launcher/ |
| H A D | LaunchAction.java | 171 …String userArgs = (info != null) ? CoreUtility.normalize(info.getCompleteProgramArguments(os, arch… in getProgramArguments() local
172 return concatArgs(buffer, userArgs); in getProgramArguments()
178 …String userArgs = (info != null) ? CoreUtility.normalize(info.getCompleteVMArguments(os, arch)) : … in getVMArguments() local
179 return concatArgs(buffer, userArgs); in getVMArguments()
182 private String concatArgs(StringBuilder initialArgs, String userArgs) { in concatArgs() argument
184 if (userArgs != null && userArgs.length() > 0) { in concatArgs()
185 List<String> userArgsList = Arrays.asList(DebugPlugin.splitArguments(userArgs)); in concatArgs()
|
| /dports/devel/spark/spark-2.1.1/yarn/src/main/scala/org/apache/spark/deploy/yarn/ |
| H A D | ClientArguments.scala | 29 var userArgs: ArrayBuffer[String] = new ArrayBuffer[String]() variable
55 userArgs += value
|
| H A D | ApplicationMasterArguments.scala | 29 var userArgs: Seq[String] = Nil variable
79 userArgs = userArgsBuffer.toList
|
| H A D | ApplicationMaster.scala | 556 val hostport = args.userArgs(0)
622 var userArgs = args.userArgs variable
626 userArgs = Seq(args.primaryPyFile, "") ++ userArgs
637 mainMethod.invoke(null, userArgs.toArray)
|
| /dports/java/openjdk17/jdk17u-jdk-17.0.1-12-1/test/lib/jdk/test/lib/ |
| H A D | Utils.java | 222 public static String[] prependTestJavaOpts(String... userArgs) { in prependTestJavaOpts() argument
225 Collections.addAll(opts, userArgs); in prependTestJavaOpts()
234 public static String[] appendTestJavaOpts(String... userArgs) { in appendTestJavaOpts() argument
236 Collections.addAll(opts, userArgs); in appendTestJavaOpts()
246 public static String[] addTestJavaOpts(String... userArgs) { in addTestJavaOpts() argument
247 return prependTestJavaOpts(userArgs); in addTestJavaOpts()
|
| /dports/java/openjdk16/jdk16u-jdk-16.0.2-7-1/test/lib/jdk/test/lib/ |
| H A D | Utils.java | 221 public static String[] prependTestJavaOpts(String... userArgs) { in prependTestJavaOpts() argument
224 Collections.addAll(opts, userArgs); in prependTestJavaOpts()
233 public static String[] appendTestJavaOpts(String... userArgs) { in appendTestJavaOpts() argument
235 Collections.addAll(opts, userArgs); in appendTestJavaOpts()
245 public static String[] addTestJavaOpts(String... userArgs) { in addTestJavaOpts() argument
246 return prependTestJavaOpts(userArgs); in addTestJavaOpts()
|
| /dports/java/openjdk15/jdk15u-jdk-15.0.6-1-1/test/lib/jdk/test/lib/ |
| H A D | Utils.java | 190 public static String[] prependTestJavaOpts(String... userArgs) { in prependTestJavaOpts() argument
193 Collections.addAll(opts, userArgs); in prependTestJavaOpts()
202 public static String[] appendTestJavaOpts(String... userArgs) { in appendTestJavaOpts() argument
204 Collections.addAll(opts, userArgs); in appendTestJavaOpts()
214 public static String[] addTestJavaOpts(String... userArgs) { in addTestJavaOpts() argument
215 return prependTestJavaOpts(userArgs); in addTestJavaOpts()
|
| /dports/java/eclipse/eclipse.platform.releng.aggregator-R4_16/eclipse.pde.ui/ui/org.eclipse.pde.launching/src/org/eclipse/pde/internal/launching/launcher/ |
| H A D | LaunchArgumentsHelper.java | 51 String[] userArgs = getUserProgramArgumentArray(configuration); in getWorkspaceLocation() local
52 for (int i = 0; i < userArgs.length; i++) { in getWorkspaceLocation()
53 …if (userArgs[i].equals("-data") && (i + 1) < userArgs.length && userArgs[i + 1].equals("@none")) {… in getWorkspaceLocation()
|
| /dports/editors/kate/kate-21.12.3/addons/compiler-explorer/ |
| H A D | ce_service.cpp | 115 const QString &userArgs, in getCompilationOptions() argument
124 optObj[QStringLiteral("userArguments")] = userArgs; in getCompilationOptions()
|
| H A D | ce_service.h | 20 const QString &userArgs,
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/cmdline/GATKPlugin/ |
| H A D | GATKReadFilterPluginDescriptorTest.java | 295 Assert.assertEquals(readFilterPlugin.userArgs.getUserDisabledReadFilterNames().size(), 1); in testDisableOneFilter()
296 Assert.assertTrue(readFilterPlugin.userArgs.getUserDisabledReadFilterNames().contains( in testDisableOneFilter()
314 Assert.assertTrue(rfDesc.userArgs.getUserDisabledReadFilterNames().contains(filterName)); in testDisableNotEnabledFilter()
351 Assert.assertEquals(readFilterPlugin.userArgs.getUserDisabledReadFilterNames().size(), 2); in testDisableMultipleFilters()
352 Assert.assertTrue(readFilterPlugin.userArgs.getUserDisabledReadFilterNames().contains( in testDisableMultipleFilters()
354 Assert.assertTrue(readFilterPlugin.userArgs.getUserDisabledReadFilterNames().contains( in testDisableMultipleFilters()
393 Assert.assertTrue(readFilterPlugin.userArgs.getDisableToolDefaultReadFilters()); in testDisableToolDefaultFilters()
443 Assert.assertTrue(rfDesc.userArgs.getUserDisabledReadFilterNames().contains(filterName)); in testDisabledDefaultWithArgsNotProvided()
|
| /dports/java/openjdk11/jdk11u-jdk-11.0.13-8-1/test/jdk/lib/testlibrary/jdk/testlibrary/ |
| H A D | Utils.java | 125 public static String[] addTestJavaOpts(String... userArgs) { in addTestJavaOpts() argument
128 Collections.addAll(opts, userArgs); in addTestJavaOpts()
|
| /dports/java/openjdk11-jre/jdk11u-jdk-11.0.13-8-1/test/jdk/lib/testlibrary/jdk/testlibrary/ |
| H A D | Utils.java | 125 public static String[] addTestJavaOpts(String... userArgs) { in addTestJavaOpts() argument
128 Collections.addAll(opts, userArgs); in addTestJavaOpts()
|
| /dports/java/openjdk8/jdk8u-jdk8u312-b07.1/hotspot/test/testlibrary/com/oracle/java/testlibrary/ |
| H A D | Utils.java | 162 public static String[] addTestJavaOpts(String... userArgs) { in addTestJavaOpts() argument
165 Collections.addAll(opts, userArgs); in addTestJavaOpts()
|
| /dports/java/openjdk8-jre/jdk8u-jdk8u312-b07.1/hotspot/test/testlibrary/com/oracle/java/testlibrary/ |
| H A D | Utils.java | 162 public static String[] addTestJavaOpts(String... userArgs) { in addTestJavaOpts() argument
165 Collections.addAll(opts, userArgs); in addTestJavaOpts()
|
| /dports/multimedia/syncplay/syncplay-1.6.4a/syncplay/players/ |
| H A D | mpv.py | 37 def getStartupArgs(path, userArgs): argument
39 if userArgs:
40 args.extend(userArgs)
|