1. 16 Jan, 2018 1 commit
  2. 07 Jul, 2017 1 commit
    • Mikaël Salson's avatar
      algo/: Refactor Fasta to BioReader · 3d8ff242
      Mikaël Salson authored
      We now have an abstract class to deal with biological sequence files. This
      will allow to more easily manage different file types.
      
      This commit only reorganizes the code so that we will be able to add a BAM
      reader easily. Functionnally the code should be equivalent to its previous
      version.
      
      Some functions that were not used have been removed.
      
      The operator>> has been removed as it was only used in unit testing. This
      operator is not convenient as having the filename may be useful to reopen the
      file or to know its extension, to guess the filetype.
      
      See #2016
      3d8ff242
  3. 14 Mar, 2017 3 commits
  4. 24 Jan, 2017 1 commit
  5. 06 Aug, 2016 1 commit
  6. 05 Aug, 2016 1 commit
  7. 25 Jul, 2016 1 commit
    • Mathieu Giraud's avatar
      core/segment.{h,cpp}: multiplier is 'double' · 37c5597e
      Mathieu Giraud authored
      A @rchikhi set with ~150M reads tested with all locus gave an e-value multiplier >2^31,
      leading to integer overflow and many spurious clones.
      
      Moreover, the previous multiplier was only an 'int', depending on the actual implementation.
      The multiplier is now a float (double) value.
      37c5597e
  8. 06 Jul, 2016 1 commit
  9. 23 Apr, 2016 2 commits
  10. 22 Apr, 2016 1 commit
  11. 01 Mar, 2016 3 commits
  12. 28 Feb, 2016 3 commits
  13. 06 Feb, 2016 3 commits
  14. 05 Feb, 2016 3 commits
  15. 02 Feb, 2016 5 commits
  16. 01 Feb, 2016 1 commit
  17. 22 Dec, 2015 2 commits
  18. 17 Dec, 2015 1 commit
  19. 12 Dec, 2015 2 commits
  20. 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
  21. 17 Oct, 2015 1 commit
  22. 18 Sep, 2015 2 commits