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  1. 28 Feb, 2016 3 commits
  2. 17 Feb, 2016 1 commit
  3. 06 Feb, 2016 5 commits
  4. 05 Feb, 2016 8 commits
  5. 02 Feb, 2016 8 commits
  6. 01 Feb, 2016 6 commits
  7. 22 Dec, 2015 2 commits
  8. 18 Dec, 2015 2 commits
  9. 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.
  10. 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.
    • Mathieu Giraud's avatar
  11. 07 Oct, 2015 2 commits