1. 10 Jul, 2018 1 commit
  2. 31 Jan, 2018 1 commit
  3. 16 Jan, 2018 1 commit
    • Mikael Salson's avatar
      core/{windowExtractor,windows,segment}: Short/shifted windows · bd1eadc7
      Mikael 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
  4. 07 Jul, 2017 1 commit
    • Mikael Salson's avatar
      algo/: Refactor Fasta to BioReader · 3d8ff242
      Mikael 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
  5. 28 Sep, 2016 2 commits
    • Mikael Salson's avatar
    • Mikael Salson's avatar
      read_score.{h,cpp}: ReadQualityScorer · e977c03c
      Mikael Salson authored
      A new score depending on quality and length
      
      The percentile of the quality is computed multiplied by the read length
      and is then divided by what we consider being a good quality.
      This somehow corresponds to artificially diminishing the read length if
      the quality is bad.
      
      We increase the number of bins to make sure that the better quality
      reads will be in a different bin than medium quality reads.
      e977c03c
  6. 27 Sep, 2016 1 commit
  7. 26 Sep, 2016 1 commit
    • Mikael Salson's avatar
      algo/{vidjil, core/{windows, windowExtractor}}: Add sequences of interest · 14602c22
      Mikael Salson authored
      DNA sequences that should be found in the window (or windows that should
      be found into it) can be kept whatever their concentration is. We
      therefore extend what is already done for labelled windows.
      
      Now the sequences do not need to be the length of the window to be found
      but they can be of any length. However we require that the sequence of
      interest contains the window (or is contained in it).
      14602c22
  8. 28 Jan, 2016 1 commit
  9. 21 May, 2015 2 commits
  10. 11 May, 2015 5 commits
  11. 17 Mar, 2015 1 commit
  12. 11 Mar, 2015 1 commit
  13. 09 Mar, 2015 6 commits
  14. 26 Feb, 2015 1 commit
  15. 06 Feb, 2015 3 commits
  16. 04 Nov, 2014 1 commit
  17. 24 Oct, 2014 1 commit
  18. 22 Oct, 2014 1 commit
  19. 02 Oct, 2014 1 commit
  20. 12 Aug, 2014 1 commit
  21. 03 Jul, 2014 2 commits
  22. 20 Feb, 2014 1 commit
    • Mathieu Giraud's avatar
      Vidjil: release 2014.02 · 113ee8ee
      Mathieu Giraud authored
      	* Refactored main vidjil.cpp (core/windows.cpp, core/windowExtractor.cpp)
      	* Removed unused html output
      	* Better json output (core/json.cpp)
      	* Updated main stdout, with representative sequence for each clone
      	* Updated parameters for FineSegmenter (delta_max) and dynprog (substition cost)
      	* Bugs closed
      113ee8ee