Searched refs:coverageCutoff (Results 1 – 7 of 7) sorted by relevance
| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/VelvetAPI/ |
| H A D | VelvetGraph.cc | 41 void VelvetGraph::removeNodes( double coverageCutoff, double longCoverageCutoff, double maxCoverage… in removeNodes() argument
48 …removeLowCoverageNodes( coverageCutoff, longCoverageCutoff, minContigKmerLength, flagExportFiltere… in removeNodes()
58 removeLowArcs(graph, coverageCutoff); in removeNodes()
62 void VelvetGraph::removeLowCoverageNodes( double coverageCutoff, double longCoverageCutoff, long mi… in removeLowCoverageNodes() argument
64 …dubious = removeLowCoverageNodesAndDenounceDubiousReads( graph, coverageCutoff, sequences, flagExp… in removeLowCoverageNodes()
104 void VelvetGraph::finalize( double coverageCutoff, double longCoverageCutoff ){ in finalize() argument
107 removeLowCoverageReferenceNodes( graph, coverageCutoff, longCoverageCutoff, sequences ); in finalize()
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| H A D | VelvetGraph.hh | 15 …void removeLowCoverageNodes( double coverageCutoff, double longCoverageCutoff, long minContigKmerL…
28 void removeNodes( double coverageCutoff, double longCoverageCutoff, double maxCoverageCutoff,
32 void finalize( double coverageCutoff, double longCoverageCutoff );
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| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/ |
| H A D | run2.c | 82 double coverageCutoff = -1; in main() local
184 sscanf(argv[arg_index], "%lf", &coverageCutoff); in main()
437 if (coverageCutoff < 0) { in main()
438 coverageCutoff = expectedCoverage / 2; in main()
443 if (coverageCutoff < 0 && estimateCutoff) in main()
444 coverageCutoff = estimated_cov(graph, directory) / 2; in main()
449 if (coverageCutoff < 0) { in main()
467 coverageCutoff, in main()
485 removeLowArcs(graph, coverageCutoff); in main()
511 removeLowCoverageReferenceNodes(graph, coverageCutoff, longCoverageCutoff, sequences); in main()
[all …]
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| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/ |
| H A D | run2.c | 75 double coverageCutoff = -1; in main() local
163 sscanf(argv[arg_index], "%lf", &coverageCutoff); in main()
379 if (coverageCutoff < 0) { in main()
380 coverageCutoff = expectedCoverage / 2; in main()
385 if (coverageCutoff < 0 && estimateCutoff) in main()
386 coverageCutoff = estimated_cov(graph, directory) / 2; in main()
391 if (coverageCutoff < 0) { in main()
408 coverageCutoff = expectedCoverageMulti[numECM - 1] / (double) 2; in main()
412 removeLowCoverageNodesAndDenounceDubiousReads(graph, coverageCutoff); in main()
526 printf("Estimated Coverage cutoff = %f\n", coverageCutoff); in main()
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| /dports/biology/velvet/velvet_1.2.10/src/ |
| H A D | run2.c | 88 double coverageCutoff = -1; in main() local
194 sscanf(argv[arg_index], "%lf", &coverageCutoff); in main()
552 if (coverageCutoff < 0) { in main()
553 coverageCutoff = expectedCoverage / 2; in main()
558 if (coverageCutoff < 0 && estimateCutoff) in main()
559 coverageCutoff = estimated_cov(graph, directory) / 2; in main()
564 if (coverageCutoff < 0) { in main()
587 coverageCutoff, in main()
605 removeLowArcs(graph, coverageCutoff); in main()
633 removeLowCoverageReferenceNodes(graph, coverageCutoff, longCoverageCutoff, sequences); in main()
[all …]
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| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Apps/ |
| H A D | meta-velvetg.cc | 112 coverageCutoff = expectedCoverages[numCoveragePeaks-1] / 2; in estimateCoverageCutoff()
116 cout << "\t" << "Coverage cutoff = " << coverageCutoff << endl; in estimateCoverageCutoff()
120 …cout << "[meta-velvetg] " << "Min. coverage cutoff for short reads = " << coverageCutoff <<… in removeNodes()
124 metaGraph->removeNodes( coverageCutoff, longCoverageCutoff, maxCoverageCutoff, in removeNodes()
135 metaGraph->finalize( coverageCutoff, longCoverageCutoff ); in finalize()
178 coverageCutoff = META_VELVET_G_PARAMETER_VALUE_NOT_SPECIFIED; in setDefaultParameters()
407 coverageCutoff = atof( val ); in setCoverageCutoff()
685 if( coverageCutoff < 0 ) in guessCoverageFlags()
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| H A D | meta-velvetg.hh | 48 double coverageCutoff; member in MetaVelvetG
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