1. 13 Jan, 2017 1 commit
    • Mikael Salson's avatar
      BinReadStorage: Make sure init() is launched just once. · 4090d73a
      Mikael Salson authored
      Launching init several times will allocate several times score_bins and nb_scores
      which will cause memory leaks.
      This is particularly the case in the WindowExtractor() which calls BinReadStorage
      on germline->code but we can have different germlines with the same germline->code.
  2. 28 Sep, 2016 4 commits
    • Mikael Salson's avatar
      windows: read must be sampled depending on the score · 3dacebba
      Mikael 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.
    • Mikael Salson's avatar
      core/read_storage, core/window: Average read length · 5bf47aae
      Mikael 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.
    • Mikael Salson's avatar
      read_storage: getBin(): access to any bin · 28614c98
      Mikael Salson authored
    • Mikael Salson's avatar
  3. 12 May, 2015 1 commit
  4. 11 May, 2015 4 commits
  5. 09 Mar, 2015 1 commit