1. 18 Oct, 2018 1 commit
  2. 16 Oct, 2018 1 commit
  3. 10 Jul, 2018 1 commit
  4. 05 Jul, 2018 4 commits
  5. 23 Jun, 2018 1 commit
  6. 18 Jun, 2018 1 commit
  7. 13 Jun, 2018 3 commits
  8. 06 Apr, 2018 2 commits
  9. 18 Jan, 2018 1 commit
  10. 17 Jan, 2018 2 commits
  11. 28 Aug, 2017 1 commit
  12. 07 Jul, 2017 2 commits
    • Mikaël Salson's avatar
      core/tools.h: Document function · 3d123f2e
      Mikaël Salson authored
      3d123f2e
    • 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
  13. 07 Mar, 2017 2 commits
    • Mikaël Salson's avatar
      tools: RATIO_TOO_MANY_N is better as an integer · 5e193fcb
      Mikaël Salson authored
      Having a float can lead to some rounding issues.
      It is thus better to have an integer, a percentage should
      be precise enough
      5e193fcb
    • Mikaël Salson's avatar
      tools.cpp: Rewrite trimSequences() · 12963427
      Mikaël Salson authored
      This is an online algorithm taking constant extra space.
      The idea is to count at each point if the prefix or the suffix
      reaches the threshold of N ratio.
      When such a threshold is reached, we cut the corresponding
      substring and keep it only if it the longest seen yet.
      
      Fixes #2217.
      12963427
  14. 27 Jan, 2017 1 commit
  15. 13 Jan, 2017 1 commit
    • Mikaël Salson's avatar
      tools: generate_all_seeds · 85455813
      Mikaël Salson authored
      Take a string and a seed (which spans the whole seed) and generates all
      the strings matching the input string with the seed.
      
      Tests included.
      85455813
  16. 01 Dec, 2016 1 commit
  17. 28 Sep, 2016 1 commit
    • Mikaël Salson's avatar
      tools: Remove Ns at the end of a sequence · 2099c49f
      Mikaël Salson authored
      We remove the longest prefix (resp. suffix) ending with a
      N (resp. starting) whose N content is greater or equal to
      RATIO_TOO_MANY_N.
      
      This is particularly useful for the representative: because of spaced
      seeds we may have N in the representative, especially on the ends of the
      representative (when only one seed matched at the extremity of the
      sequence).
      2099c49f
  18. 06 Aug, 2016 1 commit
  19. 27 Jun, 2016 1 commit
  20. 20 Jun, 2016 1 commit
  21. 28 Feb, 2016 2 commits
  22. 12 Dec, 2015 1 commit
    • Mathieu Giraud's avatar
      core/windowExtractor.cpp: do not halt when there is an error in a .fastq file · 0ce12ff5
      Mathieu Giraud authored
      The .fastq parser in OnlineFasta() is rigourous. When the file was truncated somewhere,
      there can be a non-valid sequence at the end of the file.
      
      Previously Vidjil was halting in this case, and this could be quite frustating
      when a large number of sequences were already processed. Now we just warn the user,
      stop the analysis at this point, and properly output the clones.
      
      Note that this does not affect the initial scan done on at most SAMPLE_APPROX_NB_SEQUENCES
      sequences (currently 200): Vidjil will still halt on any error in these first sequences.
      0ce12ff5
  23. 17 Oct, 2015 1 commit
  24. 16 Jul, 2015 1 commit
  25. 12 May, 2015 1 commit
  26. 11 May, 2015 2 commits
  27. 03 Apr, 2015 1 commit
  28. 02 Apr, 2015 1 commit
  29. 01 Apr, 2015 1 commit