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  1. 16 Feb, 2015 1 commit
  2. 06 Feb, 2015 1 commit
  3. 05 Feb, 2015 1 commit
    • Mikaël Salson's avatar
      MultiKmerSegmenter: Use pointer for the_kseg · f62ab84a
      Mikaël Salson authored
      Not using a pointer creates some problems with KmerSegmenter.
      We should have a copy constructor in KmerSegmenter but it is a pain in the ***.
      
      Not using pointers makes several copies of the same object. However the copies share the
      same pointer to a KmerAffectAnalyser and that's the problem. When one of the copy is
      deleted, its destructor is called which will delete the KmerAffectAnalyser and the other
      copies won't have access to it, and it will also generate an error when the copies will try
      to delete the KmerAffectAnalyser.
      
      This has been solved by using pointers to KmerSegmenter everywhere.
      f62ab84a
  4. 03 Feb, 2015 1 commit
  5. 02 Feb, 2015 2 commits
  6. 16 Dec, 2014 1 commit
  7. 03 Dec, 2014 1 commit
    • Mathieu Giraud's avatar
      core/segment.{h,cpp}: both V and J kmers must be above DETECT_THRESHOLD to... · a8df78ec
      Mathieu Giraud authored
      core/segment.{h,cpp}: both V and J kmers must be above DETECT_THRESHOLD to flag the germline as 'detected'
      
      This reverts the idea of 41b4f071, but still uses a 'detected' flag.
      This flag tells us whether we should continue to the remaining germlines.
      In the case of incomplete rearrangements, we certainly want to continue even if we have
      many V or many J (but now both of them).
      Tests d2a0dbd5 are now passing.
      
      Note that we don't run this test when strand == 2, this should be changed.
      a8df78ec
  8. 22 Nov, 2014 1 commit
    • Mathieu Giraud's avatar
      core/segment.cpp: UNSEG_AMBIGUOUS of the previous commits becomes a 'detected' flag · 41b4f071
      Mathieu Giraud authored
      ABIGUOUS_THRESHOLD becomes DETECTED_THRESHOLD, such reads are flag 'detected'
      
      This is cleaner: on one side we have the cause of unsegmentation, on the other we have the
      flag 'detected' if there were enough V+J (now total V+J, we don't need to have both V and J).
      Currently, the flag can be set when SEG_+/, TOO_FEW_V/J, or DELTA_MIN/MAX (but not STRAND).
      
      We do not continue to the remaining germlines when 'detected' or STRAND.
      41b4f071
  9. 21 Nov, 2014 1 commit
  10. 01 Nov, 2014 1 commit
  11. 20 Oct, 2014 1 commit
  12. 14 Oct, 2014 1 commit
  13. 01 Oct, 2014 3 commits
  14. 08 Aug, 2014 1 commit
  15. 07 Jul, 2014 2 commits
  16. 03 Jul, 2014 1 commit
  17. 16 May, 2014 1 commit
  18. 14 Apr, 2014 1 commit
  19. 27 Mar, 2014 1 commit
  20. 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
  21. 07 Oct, 2013 1 commit
    • Mikaël Salson's avatar
      Vidjil: release 2013.10 · 2cbd3725
      Mikaël Salson authored
      	* Better heuristic, segments more reads (core/segment.cpp)
      	* Better and faster selection of representative read (vidjil.cpp, core/read_chooser.cpp)
      	* Better display of reason of non-segmenting reads
      	* New normalization against a standard (-Z) (core/labels.cpp)
      	* New experimental lazy_msa multiple aligner
      	* New .json output
      	* New unit tests
      	* Bugs closed
      2cbd3725
  22. 26 Apr, 2013 1 commit