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  1. 08 Apr, 2015 1 commit
  2. 07 Apr, 2015 3 commits
  3. 06 Apr, 2015 2 commits
  4. 03 Apr, 2015 3 commits
  5. 01 Apr, 2015 6 commits
  6. 08 Mar, 2015 1 commit
  7. 02 Mar, 2015 1 commit
  8. 01 Mar, 2015 1 commit
  9. 26 Feb, 2015 1 commit
  10. 16 Feb, 2015 1 commit
  11. 06 Feb, 2015 1 commit
  12. 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
  13. 03 Feb, 2015 1 commit
  14. 02 Feb, 2015 2 commits
  15. 16 Dec, 2014 1 commit
  16. 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
  17. 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
  18. 21 Nov, 2014 1 commit
  19. 01 Nov, 2014 1 commit
  20. 20 Oct, 2014 1 commit
  21. 14 Oct, 2014 1 commit
  22. 01 Oct, 2014 3 commits
  23. 08 Aug, 2014 1 commit
  24. 07 Jul, 2014 2 commits
  25. 03 Jul, 2014 1 commit
  26. 16 May, 2014 1 commit