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  1. 01 Mar, 2016 1 commit
  2. 28 Feb, 2016 3 commits
  3. 06 Feb, 2016 3 commits
  4. 05 Feb, 2016 3 commits
  5. 02 Feb, 2016 5 commits
  6. 01 Feb, 2016 1 commit
  7. 22 Dec, 2015 2 commits
  8. 17 Dec, 2015 1 commit
  9. 12 Dec, 2015 2 commits
  10. 09 Nov, 2015 1 commit
    • Mathieu Giraud's avatar
      core/segment.{cpp,h}: computes only half of the DP matrix for VJ segments · 513a047b
      Mathieu Giraud authored
      Starting from the full read, we can not limit the DP computations
      to a k-band around the diagonal without first knowing where is exactly the junction.
      
      Nevertheless, we can avoid computing about one half of the DP matrix,
      as the end of the V / the start of the J (minus some deletions) must be matched.
      
      The BOTTOM_TRIANGLE_SHIFT is now set to 20, and this should be large enough
      to handle V/J deletions until ~30 bp (see comment in segment.h).
      (The current tests were even passing with BOTTOM_TRIANGLE_SHIFT set to 10.)
      
      Now the FineSegmenter (as launched by 'make shouldvdj_with_rc_merged') is about 35% faster.
      513a047b
  11. 17 Oct, 2015 1 commit
  12. 18 Sep, 2015 2 commits
  13. 16 Sep, 2015 2 commits
  14. 09 Sep, 2015 1 commit
  15. 03 Jul, 2015 4 commits
  16. 09 Jun, 2015 1 commit
  17. 28 May, 2015 1 commit
    • Mikaël Salson's avatar
      algo/: Remove delta_max, use delta_min only in FineSegmenter. · d567545c
      Mikaël Salson authored
      delta_max is now useless. It was use to make sure we didn't segment
      something not robust enough. Now we use the e-value, which is a much
      trustable value.
      
      delta_min is useless to the KmerSegmenter (we can't have overlaps
      with the first_max, last_max algorithms).
      But it can still be useful to FineSegmenter, that's why we keep it.
      d567545c
  18. 26 May, 2015 1 commit
  19. 21 May, 2015 4 commits
  20. 15 May, 2015 1 commit