Home
last modified time | relevance | path

Searched refs:minContigLength (Results 1 – 17 of 17) sorted by relevance

/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/VelvetAPI/
H A DVelvetGraph.cc42 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 …]
H A DVelvetGraph.hh14 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;
/dports/biology/abyss/abyss-2.3.1/Scaffold/
H A Dscaffold.cc102 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 …]
/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Apps/
H A Dmeta-velvetg.cc123 …<< "[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()
H A Dmeta-velvetg.hh45 long minContigLength; member in MetaVelvetG
/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/
H A Drun2.c79 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()
H A DgraphStats.h74 IDnum usedReads(Graph * graph, Coordinate minContigLength);
H A DgraphStats.c2784 IDnum usedReads(Graph * graph, Coordinate minContigLength) in usedReads() argument
2796 if (node == NULL || getNodeLength(node) < minContigLength) in usedReads()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/copynumber/plotting/
H A DPlottingUtils.java60 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()
H A DPlotDenoisedCopyRatios.java115 private int minContigLength = PlottingUtils.DEFAULT_MINIMUM_CONTIG_LENGTH; field in PlotDenoisedCopyRatios
163 …tigLengthMap = PlottingUtils.getContigLengthMap(sequenceDictionaryToPlot, minContigLength, logger); in doWork()
H A DPlotModeledSegments.java150 private int minContigLength = PlottingUtils.DEFAULT_MINIMUM_CONTIG_LENGTH; field in PlotModeledSegments
223 …tigLengthMap = PlottingUtils.getContigLengthMap(sequenceDictionaryToPlot, minContigLength, logger); in doWork()
/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/
H A Drun2.c86 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()
H A DgraphStats.h58 IDnum usedReads(Graph * graph, Coordinate minContigLength);
H A DgraphStats.c1798 IDnum usedReads(Graph * graph, Coordinate minContigLength) in usedReads() argument
1810 if (node == NULL || getNodeLength(node) < minContigLength) in usedReads()
/dports/biology/velvet/velvet_1.2.10/src/
H A Drun2.c92 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()
H A DgraphStats.h58 IDnum usedReads(Graph * graph, Coordinate minContigLength);
H A DgraphStats.c1787 IDnum usedReads(Graph * graph, Coordinate minContigLength) in usedReads() argument
1799 if (node == NULL || getNodeLength(node) < minContigLength) in usedReads()