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/dports/biology/canu/canu-2.2/src/pipelines/canu/
H A DExecution.pm280 runCommand(getGlobal("onExitDir"), getGlobal("onSuccess") . " " . getGlobal("onExitNam"));
432 my $javaPath = getGlobal("java");
715 … $gridOpts .= getGlobal("gridOptionsExecutive") if (defined(getGlobal("gridOptionsExecutive")));
717 $gridOpts .= getGlobal("gridOptions") if (defined(getGlobal("gridOptions")));
723 $gridOpts .= getGlobal("gridOptions") if (defined(getGlobal("gridOptions")));
725 … $gridOpts .= getGlobal("gridOptionsExecutive") if (defined(getGlobal("gridOptionsExecutive")));
731 $gridOpts .= getGlobal("gridOptions") if (defined(getGlobal("gridOptions")));
802 if (uc(getGlobal("gridEngine")) eq "PBSPRO" || uc(getGlobal("gridEngine")) eq "PBS") {
1272 if (getGlobal("showNext")) {
1451 if (getGlobal("showNext")) {
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H A DDefaults.pm84 sub getGlobal ($) { subroutine
103 if (!defined(getGlobal($var))) {
391 my $errors = getGlobal("errors");
577 my $val = getGlobal($var);
595 my $VAL = getGlobal($var);
1410 my $gs = getGlobal("genomeSize");
1443 elsif ((getGlobal($var) < 0.0) || (getGlobal($var) > 1.0)) {
1454 elsif ((getGlobal($var) < 0.0) || (getGlobal($var) > 1.0)) {
1470 if (getGlobal("minReadLength") < getGlobal("minOverlapLength")) {
1573 …if ((getGlobal("maxInputCoverage") > 0) && (getGlobal("maxInputCoverage") < getGlobal("minInputCov…
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H A DConfigure.pm165 my $localmem = getGlobal("localMemory");
166 my $localcpu = getGlobal("localThreads");
183 my $maxmem = getGlobal("maxMemory");
184 my $maxcpu = getGlobal("maxThreads");
220 …my $class = ((getGlobal("useGrid") ne "0") && (defined(getGlobal("gridEngine")))) ? "grid" : "loca…
231 my $minMemory = getGlobal("minMemory");
247 my $minm = getGlobal("minMemory");
248 my $mint = getGlobal("minThreads");
250 my $maxm = getGlobal("maxMemory");
251 my $maxt = getGlobal("maxThreads");
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H A DOverlapMhap.pm143 my $javaPath = getGlobal("java");
144 …my $javaOpt = "-d64" if (defined(getGlobal("javaUse64Bit")) && getGlobal("javaUse64Bit") == …
283 print F "#!" . getGlobal("shell") . "\n";
351 …print F " --no-tf \\\n" if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}M…
361 …print F " " . getGlobal("${tag}MhapOptions") . " \\\n" if (defined(getGlobal("${tag}Mhap…
386 print F "#!" . getGlobal("shell") . "\n";
470 …print F " --no-tf \\\n" if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag…
480 …print F " " . getGlobal("${tag}MhapOptions") . " \\\n" if (defined(getGlobal("${tag}Mhap…
530 if (getGlobal("${tag}ReAlign") eq "1") {
610 my $attempt = getGlobal("canuIteration");
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H A DGrid_Cloud.pm73 my $os = getGlobal("objectStore");
98 if (!defined(getGlobal("objectStore"))) {
120 if ((getGlobal("objectStore") ne "TEST") &&
121 (getGlobal("objectStore") ne "DNANEXUS")) {
176 my $dx = getGlobal("objectStoreClient");
222 my $dx = getGlobal("objectStoreClient");
224 my $pr = getGlobal("objectStoreProject");
257 my $dx = getGlobal("objectStoreClient");
277 my $dx = getGlobal("objectStoreClient");
423 my $dx = getGlobal("objectStoreClient");
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H A DUnitig.pm85 my $gs = getGlobal("genomeSize");
100 $cmd .= " -sizes -s " . getGlobal("genomeSize") . " \\\n";
193 print F "#!" . getGlobal("shell") . "\n";
226 print F " -gs " . getGlobal("genomeSize") . " \\\n";
239 …print F " -threads " . getGlobal("batThreads") . " \\\n" if (defined(getGlobal("bat…
240 …print F " -M " . getGlobal("batMemory") . " \\\n" if (defined(getGlobal("bat…
241 …print F " -unassembled " . getGlobal("contigFilter") . " \\\n" if (defined(getGlobal("con…
242 …print F " " . getGlobal("batOptions") . " \\\n" if (defined(getGlobal("bat…
270 print F " -sizes -s " . getGlobal("genomeSize") . " \\\n";
301 my $attempt = getGlobal("canuIteration");
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H A DCorrectReads.pm53 my $des = getGlobal("corOutCoverage");
78 if (!defined(getGlobal("corMinCoverage"))) {
129 …$cmd .= " -eL " . getGlobal("corMinEvidenceLength") . " \\\n" if (defined(getGlobal("corMinEvide…
130 …$cmd .= " -eE " . getGlobal("corMaxEvidenceErate") . " \\\n" if (defined(getGlobal("corMaxEvide…
262 my $maxmem = getGlobal("corMemory");
341 my $par = getGlobal("corPartitions");
342 my $rds = getGlobal("corPartitionMin");
351 print F "#!" . getGlobal("shell") . "\n";
393 print F "#!" . getGlobal("shell") . "\n";
516 my $attempt = getGlobal("canuIteration");
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H A DOverlapErrorAdjustment.pm170 my $maxReads = getGlobal("redBatchSize");
171 my $maxBases = getGlobal("redBatchLength");
270 my $batchSize = getGlobal("redBatchSize");
271 my $numThreads = getGlobal("redThreads");
275 print F "#!" . getGlobal("shell") . "\n\n";
335 my $attempt = getGlobal("canuIteration");
472 my $maxReads = getGlobal("oeaBatchSize");
473 my $maxBases = getGlobal("oeaBatchLength");
580 print F "#!" . getGlobal("shell") . "\n\n";
640 my $attempt = getGlobal("canuIteration");
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H A DConsensus.pm51 print F "#!" . getGlobal("shell") . "\n";
84 print F " -e " . getGlobal("cnsErrorRate") . " \\\n";
89 print F " -threads " . getGlobal("cnsThreads") . " \\\n";
97 if (getGlobal("canuIteration") < 0) {
130 my $np = getGlobal("cnsPartitions");
204 my $curMem = getGlobal("cnsMemory");
255 if ((getGlobal("cnsConsensus") eq "quick") ||
256 (getGlobal("cnsConsensus") eq "pbdagcon") ||
257 (getGlobal("cnsConsensus") eq "utgcns")) {
280 my $attempt = getGlobal("canuIteration");
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H A DOverlapInCore.pm94 $cmd .= " -hl " . getGlobal("${tag}OvlHashBlockLength") . " \\\n";
95 $cmd .= " -rl " . getGlobal("${tag}OvlRefBlockLength") . " \\\n";
96 $cmd .= " -ol " . getGlobal("minOverlapLength") . " \\\n";
124 my $merSize = getGlobal("${tag}OvlMerSize");
132 my $hashBits = getGlobal("${tag}OvlHashBits");
133 my $hashLoad = getGlobal("${tag}OvlHashLoad");
136 print F "#!" . getGlobal("shell") . "\n";
177 print F " -t ", getGlobal("${tag}OvlThreads"), " \\\n";
186 …print F " --minkmers \\\n" if (defined(getGlobal("${tag}OvlFilter")) && getGlobal("${tag}OvlFilte…
305 my $attempt = getGlobal("canuIteration");
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H A DGrid_SGE.pm38 return if ( defined(getGlobal("gridEngine")));
41 if (getGlobal("useGrid") eq "0") {
159 return if (uc(getGlobal("gridEngine")) ne "SGE");
161 my $maxArraySize = getGlobal("gridEngineArrayMaxJobs");
193 if (!defined(getGlobal("gridEngineResourceOption"))) {
220 my $opt = getGlobal("gridEngineResourceOption");
240 my $opt = getGlobal("gridEngineResourceOption");
295 if (getGlobal('gridOptions') !~ m/-S/) {
341 if (!defined(getGlobal('gridOptions'))) {
391 my $mm = getGlobal("maxMemory");
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H A DHaplotypeReads.pm214 my $genomeSize = getGlobal("genomeSize");
364 my $thr = getGlobal("merylThreads");
415 if (defined(getGlobal("objectStore"))) {
426 if (defined(getGlobal("objectStore"))) {
445 if (defined(getGlobal("objectStore"))) {
494 if (defined(getGlobal("objectStore"))) {
505 if (defined(getGlobal("objectStore"))) {
531 if (defined(getGlobal("objectStore"))) {
590 if (defined(getGlobal("objectStore"))) {
960 my $mem = getGlobal("hapMemory");
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H A DMeryl.pm62 if (getGlobal("${tag}Overlapper") eq "ovl") {
63 $merSize = getGlobal("${tag}OvlMerSize");
255 my $gnuplot = getGlobal("gnuplot");
390 my $mem = getGlobal("merylMemory");
391 my $thr = getGlobal("merylThreads");
395 print F "#!" . getGlobal("shell") . "\n";
534 if (defined(getGlobal("objectStore"))) {
590 if (defined(getGlobal("objectStore"))) {
683 if (defined(getGlobal("objectStore"))) {
692 if (defined(getGlobal("objectStore"))) {
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H A DOverlapStore.pm127 print F "#!" . getGlobal("shell") . "\n";
166 my $attempt = getGlobal("canuIteration");
176 if ($attempt >= getGlobal("canuIterationMax")) {
238 print F "#!" . getGlobal("shell") . "\n";
265 if (defined(getGlobal("objectStore"))) {
291 if (defined(getGlobal("objectStore"))) {
317 print F "#!" . getGlobal("shell") . "\n";
339 if (defined(getGlobal("objectStore"))) {
371 if (defined(getGlobal("objectStore"))) {
422 my $attempt = getGlobal("canuIteration");
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H A DOverlapMMap.pm85 my $minimap = getGlobal("minimap");
124 my $memorySize = getGlobal("${tag}mmapMemory");
125 my $blockPerGb = getGlobal("${tag}MMapBlockSize");
244 print F "#!" . getGlobal("shell") . "\n";
317 print F "#!" . getGlobal("shell") . "\n";
398 print F " -e " . getGlobal("${tag}OvlErrorRate");
407 if (getGlobal('purgeOverlaps') ne "never") {
416 if (getGlobal("${tag}ReAlign") eq "1") {
490 my $attempt = getGlobal("canuIteration");
535 if ($attempt >= getGlobal("canuIterationMax")) {
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H A DSequenceStore.pm140 return(int(100 * getNumberOfBasesInStore($asm, $tag) / getGlobal("genomeSize")) / 100);
283 print F "#!" . getGlobal("shell") . "\n";
293 print F " -minlength " . getGlobal("minReadLength") . " \\\n";
295 if (getGlobal("maxInputCoverage") > 0) {
296 print F " -genomesize " . getGlobal("genomeSize") . " \\\n";
297 print F " -coverage " . getGlobal("maxInputCoverage") . " \\\n";
298 print F " -bias " . getGlobal("readSamplingBias") . " \\\n";
353 if (defined(getGlobal("homoPolyCompress"))) {
372 my $mincov = getGlobal("minInputCoverage");
432 my $gnuplot = getGlobal("gnuplot");
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/dports/biology/canu/canu-2.2/src/pipelines/
H A Dcanu.pl105 print getGlobal("version") . "\n";
369 print STDERR "-- " . getGlobal("version") . "\n";
684 printf STDERR "-- corOvlErrorRate %6.4f (%6.2f%%)\n", getGlobal("corOvlErrorRate"), getGlobal("…
685 printf STDERR "-- obtOvlErrorRate %6.4f (%6.2f%%)\n", getGlobal("obtOvlErrorRate"), getGlobal("…
686 printf STDERR "-- utgOvlErrorRate %6.4f (%6.2f%%)\n", getGlobal("utgOvlErrorRate"), getGlobal("…
689 printf STDERR "-- corErrorRate %6.4f (%6.2f%%)\n", getGlobal("corErrorRate"), getGlobal("cor…
690 printf STDERR "-- obtErrorRate %6.4f (%6.2f%%)\n", getGlobal("obtErrorRate"), getGlobal("obt…
691 printf STDERR "-- utgErrorRate %6.4f (%6.2f%%)\n", getGlobal("utgErrorRate"), getGlobal("utg…
692 printf STDERR "-- cnsErrorRate %6.4f (%6.2f%%)\n", getGlobal("cnsErrorRate"), getGlobal("cns…
815 my $mincov = getGlobal("stopOnLowCoverage");
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/dports/databases/mongodb36/mongodb-src-r3.6.23/src/mongo/db/
H A Dconn_pool_options.cpp57 maxConnsPerHostParameter(ServerParameterSet::getGlobal(),
62 maxShardedConnsPerHostParameter(ServerParameterSet::getGlobal(),
67 maxInUseConnsPerHostParameter(ServerParameterSet::getGlobal(),
72 maxShardedInUseConnsPerHostParameter(ServerParameterSet::getGlobal(),
77 globalConnPoolIdleTimeoutParameter(ServerParameterSet::getGlobal(),
82 shardedConnPoolIdleTimeoutParameter(ServerParameterSet::getGlobal(),
/dports/java/openjdk11/jdk11u-jdk-11.0.13-8-1/src/jdk.scripting.nashorn/share/classes/jdk/nashorn/internal/runtime/
H A DECMAErrors.java69 return asEcmaException(Context.getGlobal(), e); in asEcmaException()
119 return syntaxError(Context.getGlobal(), msgId, args); in syntaxError()
145 return syntaxError(Context.getGlobal(), cause, msgId, args); in syntaxError()
172 return typeError(Context.getGlobal(), msgId, args); in typeError()
198 return typeError(Context.getGlobal(), cause, msgId, args); in typeError()
225 return rangeError(Context.getGlobal(), msgId, args); in rangeError()
251 return rangeError(Context.getGlobal(), cause, msgId, args); in rangeError()
278 return referenceError(Context.getGlobal(), msgId, args); in referenceError()
304 return referenceError(Context.getGlobal(), cause, msgId, args); in referenceError()
331 return uriError(Context.getGlobal(), msgId, args); in uriError()
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/dports/java/openjdk13/jdk13u-jdk-13.0.10-1-1/src/jdk.scripting.nashorn/share/classes/jdk/nashorn/internal/runtime/
H A DECMAErrors.java69 return asEcmaException(Context.getGlobal(), e); in asEcmaException()
119 return syntaxError(Context.getGlobal(), msgId, args); in syntaxError()
145 return syntaxError(Context.getGlobal(), cause, msgId, args); in syntaxError()
172 return typeError(Context.getGlobal(), msgId, args); in typeError()
198 return typeError(Context.getGlobal(), cause, msgId, args); in typeError()
225 return rangeError(Context.getGlobal(), msgId, args); in rangeError()
251 return rangeError(Context.getGlobal(), cause, msgId, args); in rangeError()
278 return referenceError(Context.getGlobal(), msgId, args); in referenceError()
304 return referenceError(Context.getGlobal(), cause, msgId, args); in referenceError()
331 return uriError(Context.getGlobal(), msgId, args); in uriError()
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/dports/java/openjdk11-jre/jdk11u-jdk-11.0.13-8-1/src/jdk.scripting.nashorn/share/classes/jdk/nashorn/internal/runtime/
H A DECMAErrors.java69 return asEcmaException(Context.getGlobal(), e); in asEcmaException()
119 return syntaxError(Context.getGlobal(), msgId, args); in syntaxError()
145 return syntaxError(Context.getGlobal(), cause, msgId, args); in syntaxError()
172 return typeError(Context.getGlobal(), msgId, args); in typeError()
198 return typeError(Context.getGlobal(), cause, msgId, args); in typeError()
225 return rangeError(Context.getGlobal(), msgId, args); in rangeError()
251 return rangeError(Context.getGlobal(), cause, msgId, args); in rangeError()
278 return referenceError(Context.getGlobal(), msgId, args); in referenceError()
304 return referenceError(Context.getGlobal(), cause, msgId, args); in referenceError()
331 return uriError(Context.getGlobal(), msgId, args); in uriError()
[all …]
/dports/java/openjdk12/openjdk-jdk12u-jdk-12.0.2-10-4/src/jdk.scripting.nashorn/share/classes/jdk/nashorn/internal/runtime/
H A DECMAErrors.java69 return asEcmaException(Context.getGlobal(), e); in asEcmaException()
119 return syntaxError(Context.getGlobal(), msgId, args); in syntaxError()
145 return syntaxError(Context.getGlobal(), cause, msgId, args); in syntaxError()
172 return typeError(Context.getGlobal(), msgId, args); in typeError()
198 return typeError(Context.getGlobal(), cause, msgId, args); in typeError()
225 return rangeError(Context.getGlobal(), msgId, args); in rangeError()
251 return rangeError(Context.getGlobal(), cause, msgId, args); in rangeError()
278 return referenceError(Context.getGlobal(), msgId, args); in referenceError()
304 return referenceError(Context.getGlobal(), cause, msgId, args); in referenceError()
331 return uriError(Context.getGlobal(), msgId, args); in uriError()
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/dports/java/openjdk14/jdk14u-jdk-14.0.2-12-1/src/jdk.scripting.nashorn/share/classes/jdk/nashorn/internal/runtime/
H A DECMAErrors.java69 return asEcmaException(Context.getGlobal(), e); in asEcmaException()
119 return syntaxError(Context.getGlobal(), msgId, args); in syntaxError()
145 return syntaxError(Context.getGlobal(), cause, msgId, args); in syntaxError()
172 return typeError(Context.getGlobal(), msgId, args); in typeError()
198 return typeError(Context.getGlobal(), cause, msgId, args); in typeError()
225 return rangeError(Context.getGlobal(), msgId, args); in rangeError()
251 return rangeError(Context.getGlobal(), cause, msgId, args); in rangeError()
278 return referenceError(Context.getGlobal(), msgId, args); in referenceError()
304 return referenceError(Context.getGlobal(), cause, msgId, args); in referenceError()
331 return uriError(Context.getGlobal(), msgId, args); in uriError()
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/dports/java/openjdk8/jdk8u-jdk8u312-b07.1/nashorn/src/jdk/nashorn/internal/runtime/
H A DECMAErrors.java69 return asEcmaException(Context.getGlobal(), e); in asEcmaException()
119 return syntaxError(Context.getGlobal(), msgId, args); in syntaxError()
145 return syntaxError(Context.getGlobal(), cause, msgId, args); in syntaxError()
172 return typeError(Context.getGlobal(), msgId, args); in typeError()
198 return typeError(Context.getGlobal(), cause, msgId, args); in typeError()
225 return rangeError(Context.getGlobal(), msgId, args); in rangeError()
251 return rangeError(Context.getGlobal(), cause, msgId, args); in rangeError()
278 return referenceError(Context.getGlobal(), msgId, args); in referenceError()
304 return referenceError(Context.getGlobal(), cause, msgId, args); in referenceError()
331 return uriError(Context.getGlobal(), msgId, args); in uriError()
[all …]
/dports/java/openjdk8-jre/jdk8u-jdk8u312-b07.1/nashorn/src/jdk/nashorn/internal/runtime/
H A DECMAErrors.java69 return asEcmaException(Context.getGlobal(), e); in asEcmaException()
119 return syntaxError(Context.getGlobal(), msgId, args); in syntaxError()
145 return syntaxError(Context.getGlobal(), cause, msgId, args); in syntaxError()
172 return typeError(Context.getGlobal(), msgId, args); in typeError()
198 return typeError(Context.getGlobal(), cause, msgId, args); in typeError()
225 return rangeError(Context.getGlobal(), msgId, args); in rangeError()
251 return rangeError(Context.getGlobal(), cause, msgId, args); in rangeError()
278 return referenceError(Context.getGlobal(), msgId, args); in referenceError()
304 return referenceError(Context.getGlobal(), cause, msgId, args); in referenceError()
331 return uriError(Context.getGlobal(), msgId, args); in uriError()
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