1. 13 Jun, 2018 3 commits
  2. 29 Jan, 2018 1 commit
  3. 28 Jan, 2018 1 commit
  4. 17 Jan, 2018 4 commits
  5. 16 Jan, 2018 4 commits
    • Mikaël Salson's avatar
      core/{windowExtractor,windows,segment}: Short/shifted windows · bd1eadc7
      Mikaël Salson authored
      Warn when we have one.
      
      This requires to add a new segmentation status. The problem is that
      Segment::getSegmentationStatus() returns just an integer which doesn't make
      possible to have several statuses at once (which could be convenient). A
      solution would be to use masks for the statuses (ie. if s is the status we
      would store 1 << s).  Since this would require quite some code modification to
      achieve that, I added some extra tests (that's bad) to deal with the case
      where the segmentation is achieved with a shorter or shifted window. In such a
      case we warn the user in the JSON (warning on the CLI should be done too).
      
      See #2913, #2916.
      bd1eadc7
    • Mikaël Salson's avatar
      core/segment: Store if the window has been shifted/shortened · 57d31ed2
      Mikaël Salson authored
      It is good to know so that we can warn the user.
      
      See #2913
      57d31ed2
    • Mikaël Salson's avatar
      segment.h: The minimal window length was actually quite small. · 8aa67229
      Mikaël Salson authored
      It was hard to make some tests (eg. unsegmentation-causes.should-get) have a
      too short window. Modifying a constant just so that the test passes is bad
      practice, but this is not the case here (at least I believe so).  Having
      difficulties to have a too short w also meant that in practice we would almost
      never see a “too short w” again. This could be nice. But we know that the
      position of the window is not accurate (it is not designed to be). Therefore
      20nt, if they are perfectly centered may be ok. But we know that it may not be
      well centered (and we even allow some shifts). Therefore 30nt seems to be a
      safer limit.
      
      See #2913
      8aa67229
    • Mikaël Salson's avatar
  6. 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
  7. 14 Mar, 2017 3 commits
  8. 24 Jan, 2017 1 commit
  9. 06 Aug, 2016 1 commit
  10. 05 Aug, 2016 1 commit
  11. 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
  12. 06 Jul, 2016 1 commit
  13. 23 Apr, 2016 2 commits
  14. 22 Apr, 2016 1 commit
  15. 01 Mar, 2016 3 commits
  16. 28 Feb, 2016 3 commits
  17. 06 Feb, 2016 3 commits
  18. 05 Feb, 2016 3 commits
  19. 02 Feb, 2016 3 commits