Searched refs:ContigPaths (Results 1 – 12 of 12) sorted by relevance
/dports/biology/abyss/abyss-2.3.1/MergePaths/ |
H A D | MergeContigs.cpp | 316 typedef vector<ContigPath> ContigPaths; typedef 321 static ContigPaths 334 ContigPaths paths; in readPaths() 364 seenContigs(vector<bool>& seen, const ContigPaths& paths) in seenContigs() 366 for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) in seenContigs() 378 for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { in markRemovedContigs() 392 const ContigPaths& paths, in outputGraph() 399 for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { in outputGraph() 410 for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { in outputGraph() 590 ContigPaths paths = readPaths(mergedPathFile, &pathIDs); in main() [all …]
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H A D | MergePaths.cpp | 159 buildAssembledLengthHistogram(const Lengths& lengths, const ContigPaths& paths) in buildAssembledLengthHistogram() 166 for (ContigPaths::const_iterator pathIt = paths.begin(); pathIt != paths.end(); ++pathIt) { in buildAssembledLengthHistogram() 191 reportAssemblyMetrics(const Lengths& lengths, const ContigPaths& paths) in reportAssemblyMetrics() 433 typedef vector<ContigPath> ContigPaths; typedef 438 static ContigPaths 439 mergeSeedPaths(const Lengths& lengths, const ContigPathMap& paths, const ContigPaths& seedPaths) in mergeSeedPaths() 444 ContigPaths out; in mergeSeedPaths() 446 for (ContigPaths::const_iterator it = seedPaths.begin(); it != seedPaths.end(); ++it) in mergeSeedPaths() 767 ContigPaths seedPaths; in assemblePathGraph() 769 ContigPaths mergedPaths = mergeSeedPaths(lengths, paths, seedPaths); in assemblePathGraph() [all …]
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H A D | PathConsensus.cpp | 181 typedef vector<Path> ContigPaths; typedef 220 static ContigPaths readPaths(const string& inPath, in readPaths() 233 ContigPaths paths; in readPaths() 437 const ContigPaths& solutions, ofstream& out) in alignPair() 718 ContigPaths solutions; in fillGap() 724 for (ContigPaths::iterator solIt = solutions.begin(); in fillGap() 878 ContigPaths paths = readPaths(allPaths, pathIDs, isAmbPath); in main() 938 for (ContigPaths::const_iterator path = paths.begin(); in main()
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/dports/biology/abyss/abyss-2.3.1/Graph/ |
H A D | ConstrainedSearch.h | 25 typedef std::vector<ContigPath> ContigPaths; typedef 62 ContigPath& path, ContigPaths& solutions, in constrainedSearch() 127 Constraints& constraints, ContigPaths& paths, in constrainedSearch()
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H A D | GraphAlgorithms.h | 151 ContigPaths cp; in find_complex_transitive_edges()
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/dports/biology/abyss/abyss-2.3.1/SimpleGraph/ |
H A D | SimpleGraph.cpp | 238 const ContigPaths& solutions) in findRepeats() 241 for (ContigPaths::const_iterator solIt = solutions.begin(); in findRepeats() 325 const ContigNode& origin, const ContigPaths& paths) in constructAmbiguousPath() 332 for (ContigPaths::const_iterator it = paths.begin() + 1; in constructAmbiguousPath() 343 for (ContigPaths::const_iterator solIter = paths.begin(); in constructAmbiguousPath() 365 for (ContigPaths::const_iterator solIter = paths.begin(); in constructAmbiguousPath() 487 ContigPaths solutions; in handleEstimate() 506 for (ContigPaths::iterator solIter = solutions.begin(); in handleEstimate() 568 ContigPaths::iterator bestSol = solutions.end(); in handleEstimate() 570 for (ContigPaths::iterator solIter = solutions.begin(); in handleEstimate()
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/dports/biology/abyss/abyss-2.3.1/Layout/ |
H A D | layout.cc | 277 typedef vector<ContigPath> ContigPaths; in main() typedef 280 ContigPaths paths; in main() 285 for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) in main()
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/dports/biology/abyss/abyss-2.3.1/RResolver/ |
H A D | Contigs.h | 49 typedef std::vector<ContigPath> ContigPaths; typedef
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H A D | Contigs.cpp | 203 ContigPaths paths; in assembleContigs()
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/dports/biology/abyss/abyss-2.3.1/PopBubbles/ |
H A D | PopBubbles.cpp | 690 typedef vector<ContigPath> ContigPaths; in main() typedef 691 ContigPaths paths; in main() 699 for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { in main() 710 for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { in main()
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/dports/biology/abyss/abyss-2.3.1/Scaffold/ |
H A D | scaffold.cc | 626 typedef vector<ContigPath> ContigPaths; typedef 633 buildScaffoldLengthHistogram(Graph& g, const ContigPaths& paths) in buildScaffoldLengthHistogram() 645 for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { in buildScaffoldLengthHistogram() 794 ContigPaths paths; in scaffold() 799 for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) in scaffold()
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/dports/biology/abyss/abyss-2.3.1/FilterGraph/ |
H A D | FilterGraph.cc | 818 typedef vector<ContigPath> ContigPaths; in main() typedef 819 ContigPaths paths; in main() 825 for (ContigPaths::const_iterator it = paths.begin(); it != paths.end(); ++it) { in main()
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