1. 20 Jun, 2016 1 commit
  2. 18 Dec, 2015 1 commit
  3. 15 Jun, 2015 4 commits
  4. 12 Jun, 2015 1 commit
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  13. 19 Mar, 2015 1 commit
  14. 11 Mar, 2015 1 commit
    • Mathieu Giraud's avatar
      core/kmerstore.h: ignore all k-mers with extended nucleotides when updating index · b0e3045d
      Mathieu Giraud authored
      There are some 'N' and other extended nucleotides in the germline sequences.
      As we store in the indexes both the k-mers and their reverse complement, and as
      we handle extended nucleotides almost randomly (see tools:nuc_to_int()),
      we may have slight differences when analyzing some reads and their reverse complement.
      Ignoring such k-mers allow thus to be more deterministic, getting the same
      results on a (pure ACGT) read and its reverse complement.
      
      Another option (harder to implement) could be to add several k-mers in the index,
      but this would decrease the effective weight of the seed.
      
      Note that we should also improve the analysis of reads that includes extended nucleotides.
      b0e3045d
  15. 04 Nov, 2014 1 commit
  16. 20 Oct, 2014 3 commits
  17. 25 Jul, 2014 3 commits
  18. 24 Jul, 2014 3 commits
  19. 26 Jun, 2014 1 commit
  20. 25 Mar, 2014 1 commit
  21. 20 Mar, 2014 1 commit
  22. 20 Feb, 2014 1 commit
    • Mathieu Giraud's avatar
      Vidjil: release 2014.02 · 113ee8ee
      Mathieu Giraud authored
      	* Refactored main vidjil.cpp (core/windows.cpp, core/windowExtractor.cpp)
      	* Removed unused html output
      	* Better json output (core/json.cpp)
      	* Updated main stdout, with representative sequence for each clone
      	* Updated parameters for FineSegmenter (delta_max) and dynprog (substition cost)
      	* Bugs closed
      113ee8ee
  23. 26 Apr, 2013 1 commit