/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/VelvetAPI/ |
H A D | VelvetGraph.cc | 42 long minContigLength, bool flagExportFilteredNodes, in removeNodes() argument 45 long minContigKmerLength = getMinimumContigKmerLength( minContigLength ); in removeNodes() 76 long VelvetGraph::getMinimumContigKmerLength( long minContigLength ) const { in getMinimumContigKmerLength() 77 if( minContigLength < 2 * getWordLength(graph) ){ in getMinimumContigKmerLength() 80 return minContigLength - getWordLength(graph) + 1; in getMinimumContigKmerLength() 115 long minContigKmerLength = getMinimumContigKmerLength( minContigLength ); in save() 125 long minContigKmerLength = getMinimumContigKmerLength( minContigLength ); in saveAlignments() 129 void VelvetGraph::saveAmos( const string& amosFileName, long minContigLength ) const { in saveAmos() 130 long minContigKmerLength = getMinimumContigKmerLength( minContigLength ); in saveAmos() 134 void VelvetGraph::saveUnusedReads( const string& prefix, long minContigLength ) const { in saveUnusedReads() [all …]
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H A D | VelvetGraph.hh | 14 long getMinimumContigKmerLength( long minContigLength ) const; 34 void save( const string& graphFileName, long minContigLength, double coverageMask ) const; 36 …void saveAlignments( const string& alignmentFileName, long minContigLength, const string& seqFileN… 37 void saveAmos( const string& amosFileName, long minContigLength ) const; 38 void saveUnusedReads( const string& prefix, long minContigLength ) const;
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/dports/biology/abyss/abyss-2.3.1/Scaffold/ |
H A D | scaffold.cc | 102 static unsigned minContigLength = 1000; variable 232 if (g[u].length < minContigLength) in filterGraph() 734 filterGraph(g, minEdgeWeight, minContigLength); in scaffold() 840 minContigLength, in scaffold() 884 unsigned minContigLength, in optimize_n() argument 906 std::pair<unsigned, unsigned> minContigLength, in optimize_s() argument 936 std::pair<unsigned, unsigned> minContigLength) in optimize_grid_search() argument 961 std::pair<unsigned, unsigned> minContigLength) in optimize_line_search() argument 981 best = optimize_s(g, best.n, minContigLength, memo); in optimize_line_search() 1046 arg >> opt::minContigLength; 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 | 123 …<< "[meta-velvetg] " << "Min. contig length = " << minContigLength << end… in removeNodes() 125 minContigLength, flagExportFilteredNodes, in removeNodes() 139 metaGraph->save( FileNameUtils::getScaffoldFileName(prefix), minContigLength, coverageMask ); in output() 142 …aGraph->saveAlignments( FileNameUtils::getAlignmentFileName(prefix), minContigLength, FileNameUtil… in output() 143 …flagExportAmos ){ metaGraph->saveAmos( FileNameUtils::getAmosFileName(prefix), minContigLength ); } in output() 144 if( flagExportUnusedReads ){ metaGraph->saveUnusedReads( prefix, minContigLength ); } in output() 176 minContigLength = META_VELVET_G_PARAMETER_VALUE_NOT_SPECIFIED; in setDefaultParameters() 491 minContigLength = atoi( val ); in setMinContigLength()
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H A D | meta-velvetg.hh | 45 long minContigLength; member in MetaVelvetG
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/ |
H A D | run2.c | 79 Coordinate minContigLength = -1; in main() local 236 minContigLength = (Coordinate) longlong_var; in main() 429 if (minContigLength < 2 * getWordLength(graph)) in main() 432 minContigKmerLength = minContigLength - getWordLength(graph) + 1; in main() 491 if (minContigLength < 2 * getWordLength(graph)) in main() 494 minContigKmerLength = minContigLength - getWordLength(graph) + 1; in main()
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H A D | graphStats.h | 74 IDnum usedReads(Graph * graph, Coordinate minContigLength);
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H A D | graphStats.c | 2784 IDnum usedReads(Graph * graph, Coordinate minContigLength) in usedReads() argument 2796 if (node == NULL || getNodeLength(node) < minContigLength) in usedReads()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/plotting/ |
H A D | PlottingUtils.java | 60 final int minContigLength, in getContigLengthMap() argument 63 ParamUtils.isPositiveOrZero(minContigLength, "Minimum contig length must be non-negative."); in getContigLengthMap() 68 .filter(s -> s.getSequenceLength() >= minContigLength) in getContigLengthMap()
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H A D | PlotDenoisedCopyRatios.java | 115 private int minContigLength = PlottingUtils.DEFAULT_MINIMUM_CONTIG_LENGTH; field in PlotDenoisedCopyRatios 163 …tigLengthMap = PlottingUtils.getContigLengthMap(sequenceDictionaryToPlot, minContigLength, logger); in doWork()
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H A D | PlotModeledSegments.java | 150 private int minContigLength = PlottingUtils.DEFAULT_MINIMUM_CONTIG_LENGTH; field in PlotModeledSegments 223 …tigLengthMap = PlottingUtils.getContigLengthMap(sequenceDictionaryToPlot, minContigLength, logger); in doWork()
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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 | 86 Coordinate minContigLength = -1; in main() local 283 minContigLength = (Coordinate) longlong_var; in main() 460 if (minContigLength < 2 * getWordLength(graph)) in main() 463 minContigKmerLength = minContigLength - getWordLength(graph) + 1; in main()
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H A D | graphStats.h | 58 IDnum usedReads(Graph * graph, Coordinate minContigLength);
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H A D | graphStats.c | 1798 IDnum usedReads(Graph * graph, Coordinate minContigLength) in usedReads() argument 1810 if (node == NULL || getNodeLength(node) < minContigLength) in usedReads()
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/dports/biology/velvet/velvet_1.2.10/src/ |
H A D | run2.c | 92 Coordinate minContigLength = -1; in main() local 293 minContigLength = (Coordinate) longlong_var; in main() 580 if (minContigLength < 2 * getWordLength(graph)) in main() 583 minContigKmerLength = minContigLength - getWordLength(graph) + 1; in main()
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H A D | graphStats.h | 58 IDnum usedReads(Graph * graph, Coordinate minContigLength);
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H A D | graphStats.c | 1787 IDnum usedReads(Graph * graph, Coordinate minContigLength) in usedReads() argument 1799 if (node == NULL || getNodeLength(node) < minContigLength) in usedReads()
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