1. 29 Jan, 2016 3 commits
  2. 26 Jan, 2016 1 commit
  3. 20 Jan, 2016 1 commit
  4. 14 Jan, 2016 1 commit
  5. 09 Dec, 2015 1 commit
  6. 06 Dec, 2015 1 commit
  7. 05 Dec, 2015 1 commit
  8. 25 Nov, 2015 1 commit
  9. 18 Nov, 2015 1 commit
  10. 12 Nov, 2015 1 commit
  11. 08 Nov, 2015 6 commits
    • Rayan Chikhi's avatar
      had to suspiciously change a unit test so that it works. hope i didn't mess... · c281fa83
      Rayan Chikhi authored
      had to suspiciously change a unit test so that it works. hope i didn't mess up. it has to do with getNodes() and how it is implemented with respect to DIR_INCOMING.
    • Rayan Chikhi's avatar
      fixed the largeint bug, added a unit test · d2c367e1
      Rayan Chikhi authored
    • Rayan Chikhi's avatar
      minor · ccf5e781
      Rayan Chikhi authored
    • Rayan Chikhi's avatar
      got rid of old template specializations for Graph -- API changed a bit. · e8c2f6ef
      Rayan Chikhi authored
      getting rid of Instantiations.hpp/cpp
    • Rayan Chikhi's avatar
    • Rayan Chikhi's avatar
      this is THE big commit for GATB-core of november 2015. changelog is: · 223f9743
      Rayan Chikhi authored
      - Graph simplifications are moved from Minia to GATB-core. Call them using: graph.simplify()
      - New data structure for faster neighborhood queries. Enable it using: graph.precomputeAdjacency()
      - As a consequence of optimizations, it is now much faster to call indegree(node), outdegree(node) and
      degree(node,size_t &in,size_t &out) rather than neighbors(node, direction).size() if you're only interested
      in degrees.
      - LargeInt (the type of kmer) constructor has been removed, for speed reasons. Be warned that it might
      break existing code that implicitly rely on 0-initialization of kmers, but problems can hopefully be detected using valgrind.
      - Graph becomes GraphTemplate<Node,Edge,GraphDataVariant>, and compatibility is preserved via typedefs
      - This enables to define GraphFast<span>, a graph object which only holds Node's and Edge's for a single k-mer size,
      as opposed to a boost::variant of multiple kmer sizes before. It is faster.
      - Graph API has been changed:
      neighbors<Node> becomes neighbors,
      neighbors<Edge> becomes neighborsEdge,
      iterator<Node> becomes iterator,
      iterator<BranchingNode> becomes iteratorBranching
      - The change above was necessary, because it is difficult to specialize nested templates in C++. Actually, not all templated
      graph functions have been un-templated (because some aren't used in conjunction with GraphFast). There is still work to do.
      - Due to graph template, the following classes have also been changed to be also templatized: BranchingAlgorithm, all Frontline's, all Terminator's
      typedef's have been created to preserve compatibility
      - For speed of tools, it is now advised to follow Minia.cpp's functor technique and use GraphFast<span> instead of Graph. However
      Graph should still work and offer same performance as before.
      - GraphData is moved from Graph.cpp to Graph.hpp
      - MPHF index of a node is now cached in the Node object
      - because of that, 'const Node&' should now be just 'Node&', everywhere.
      - added a function graph.disableNodeState() to disable recording node state (normal, deleted, marked).
      Graph then avoids making MPHF queries when checking if a node exists (also involved in neighbors() queries).
      This makes the bloom flavor of graphs faster, but once precomputeAdjacency() is called, it is not relevant anymore.
      - added scripts/parse_gcc_output.py for visual inspection of gcc compilation/link errors involving graph templates
      - slightly modified src/CMakeLists so that tools may set their own KSIZE_DEFAULT_LIST (e.g. Minia)
      - speedup to LargeInt::hash1()
      - a few unit tests have been added, as well as one benchmark significantly improved: bench_graph.cpp
      - added minimizer stuff that was missing from last commit (some bugfixes, and also specialization to LargeInt<1>)
      - LargeInt's are not instances of ArrayData anymore. Instead, ArrayData is a member. This is faster.
  12. 19 Oct, 2015 1 commit
  13. 12 Oct, 2015 1 commit
  14. 11 Oct, 2015 1 commit
  15. 09 Oct, 2015 1 commit
  16. 03 Oct, 2015 1 commit
  17. 02 Oct, 2015 1 commit
  18. 27 Sep, 2015 2 commits
  19. 02 Aug, 2015 1 commit
  20. 22 May, 2015 1 commit
  21. 20 May, 2015 1 commit
  22. 13 May, 2015 4 commits
  23. 12 May, 2015 4 commits
  24. 04 May, 2015 1 commit
  25. 30 Apr, 2015 2 commits