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Searched refs:ContigPaths (Results 1 – 12 of 12) sorted by relevance

/dports/biology/abyss/abyss-2.3.1/MergePaths/
H A DMergeContigs.cpp316 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()
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H A DMergePaths.cpp159 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()
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H A DPathConsensus.cpp181 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()
/dports/biology/abyss/abyss-2.3.1/Graph/
H A DConstrainedSearch.h25 typedef std::vector<ContigPath> ContigPaths; typedef
62 ContigPath& path, ContigPaths& solutions, in constrainedSearch()
127 Constraints& constraints, ContigPaths& paths, in constrainedSearch()
H A DGraphAlgorithms.h151 ContigPaths cp; in find_complex_transitive_edges()
/dports/biology/abyss/abyss-2.3.1/SimpleGraph/
H A DSimpleGraph.cpp238 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()
/dports/biology/abyss/abyss-2.3.1/Layout/
H A Dlayout.cc277 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()
/dports/biology/abyss/abyss-2.3.1/RResolver/
H A DContigs.h49 typedef std::vector<ContigPath> ContigPaths; typedef
H A DContigs.cpp203 ContigPaths paths; in assembleContigs()
/dports/biology/abyss/abyss-2.3.1/PopBubbles/
H A DPopBubbles.cpp690 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()
/dports/biology/abyss/abyss-2.3.1/Scaffold/
H A Dscaffold.cc626 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()
/dports/biology/abyss/abyss-2.3.1/FilterGraph/
H A DFilterGraph.cc818 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()