1. 16 Oct, 2018 1 commit
  2. 11 Oct, 2018 1 commit
  3. 28 Jul, 2018 1 commit
  4. 17 Jul, 2018 1 commit
  5. 10 Jul, 2018 2 commits
  6. 31 Jan, 2018 1 commit
  7. 28 Jan, 2018 1 commit
  8. 19 Jan, 2018 1 commit
  9. 16 Jan, 2018 1 commit
    • 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
  10. 28 Sep, 2016 3 commits
    • Mikaël Salson's avatar
    • Mikaël Salson's avatar
      windows: read must be sampled depending on the score · 3dacebba
      Mikaël Salson authored
      The sample was constituted only on the sequence length which made sense
      when the reads were stored depending on their length. But now the scoring
      function changed and we focus on quality. It does not make sense anymore
      to retrieve the longest reads then. We just want to have a sample of the
      best reads (ie. those of better quality).
      
      Using that, if we change our scoring function again, no modification
      will be needed.
      
      Note that the second parameter of getBestReads() is not used yet.
      It may be useful to prevent too bad sequences to be sampled.
      
      SequenceSampler is not used anymore. It will be removed in a future release.
      3dacebba
    • Mikaël Salson's avatar
      core/read_storage, core/window: Average read length · 5bf47aae
      Mikaël Salson authored
      The average read length was obtained through getAverageScore() which is
      not very robust as nothing guarantees the score to be the read length.
      There is now a method in ReadStorage to get the average read length
      which can be called from the outside.
      5bf47aae
  11. 27 Sep, 2016 1 commit
  12. 26 Sep, 2016 1 commit
    • Mikaël Salson's avatar
      algo/{vidjil, core/{windows, windowExtractor}}: Add sequences of interest · 14602c22
      Mikaël 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
  13. 22 Feb, 2016 1 commit
  14. 28 Jan, 2016 1 commit
  15. 28 May, 2015 1 commit
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  17. 11 May, 2015 6 commits
  18. 17 Mar, 2015 1 commit
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  20. 09 Mar, 2015 7 commits
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  22. 26 Feb, 2015 1 commit
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  24. 07 Nov, 2014 1 commit