1. 06 Feb, 2016 1 commit
  2. 05 Feb, 2016 8 commits
  3. 02 Feb, 2016 8 commits
  4. 01 Feb, 2016 6 commits
  5. 22 Dec, 2015 2 commits
  6. 18 Dec, 2015 2 commits
  7. 12 Dec, 2015 1 commit
    • Mathieu Giraud's avatar
      core/segment.cpp: UNSEG_ONLY_V/J only when there are enough V/J k-mers detected · 5298c86f
      Mathieu Giraud authored
      There are two places where the segmentation can fail with UNSEG_ONLY_V/J.
      The first one, when there is no segmentation point, previously returned UNSEG_ONLY_V/J
      even when there was only one (possibly noisy) V/J k-mer.
      
      This is now corrected, UNSEG_ONLY_V/J is triggered only when one has at least DETECT_THRESHOLD k-mers (now 5).
      Ideally, we should use here an e-value check, but the segmentation point returned by kaa->getMaximum()
      is not really meaningfull in these cases and my lead to false statistics computations.
      5298c86f
  8. 09 Nov, 2015 2 commits
    • 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
    • Mathieu Giraud's avatar
      57be3d55
  9. 07 Oct, 2015 3 commits
  10. 03 Oct, 2015 2 commits
  11. 25 Sep, 2015 1 commit
  12. 18 Sep, 2015 3 commits
  13. 16 Sep, 2015 1 commit
    • Mathieu Giraud's avatar
      core/segment.cpp: best_overlap_split, redesign and new computation · 185c3bd9
      Mathieu Giraud authored
      There were several problems in the previous implementation. Now:
       - We handle separetly numbers of nucleotides in seq_{left,right} and in ref_{left,right};
       - There is no need to handle equality cases (if is the responsability of the segment_cost);
       - There is no need anymore to call dp.backtrack() (we directly use dp.best_score_on_i).
       - We also properly update del_D_left and del_D_right for VDJ recombinations
      
      The tests added in 3c138657 are now passing.
      185c3bd9