1. 28 Feb, 2015 4 commits
  2. 26 Feb, 2015 7 commits
  3. 20 Feb, 2015 3 commits
  4. 17 Feb, 2015 2 commits
  5. 16 Feb, 2015 1 commit
  6. 09 Feb, 2015 4 commits
    • Mikaël Salson's avatar
      ReadChooser: Useless comment removed. · efb822ee
      Mikaël Salson authored
      ReadChooser doesn't use a file.
      efb822ee
    • Mikaël Salson's avatar
      ReadChooser: Speed-up ReadChooser, hence representative computation. · 10108137
      Mikaël Salson authored
      ReadChooser was storing all the sequences and score in a map (log-time access)
      and then reads were stored in a vector which was sorted depending on the
      scores stored in the map. So we had many allocations (map+vector) and a slow
      access (log access time, so the sort was in n log²n, where n is the number of
      sequences). I'm a bit ashamed to have done such an inefficient thing.
      
      Now the scores and the sequences are stored in an array. The sequences
      are not copied, but just a pointer to them is stored.
      
      The C function qsort is used because the C++ sort doesn't work
      (because of implicit destruction of something).
      
      The code is now much quicker (a -c clones of 600k reads, with -z 1 is now twice as fast).
      
      Someone motivated could probably do better with a radix sort.
      10108137
    • Mikaël Salson's avatar
      Germline: remove debug info · 2b901b58
      Mikaël Salson authored
      2b901b58
    • Mikaël Salson's avatar
      Representative: Remove quality information · f4eddb24
      Mikaël Salson authored
      For the moment the representative doesn't compute
      a quality.
      
      Since we copy the information from the best sequence if the sequence had
      quality information, we were also getting it for the representative... and it
      was displayed in the .vdj.fa file.
      f4eddb24
  7. 07 Feb, 2015 7 commits
  8. 06 Feb, 2015 6 commits
  9. 05 Feb, 2015 1 commit
    • Mikaël Salson's avatar
      MultiKmerSegmenter: Use pointer for the_kseg · f62ab84a
      Mikaël Salson authored
      Not using a pointer creates some problems with KmerSegmenter.
      We should have a copy constructor in KmerSegmenter but it is a pain in the ***.
      
      Not using pointers makes several copies of the same object. However the copies share the
      same pointer to a KmerAffectAnalyser and that's the problem. When one of the copy is
      deleted, its destructor is called which will delete the KmerAffectAnalyser and the other
      copies won't have access to it, and it will also generate an error when the copies will try
      to delete the KmerAffectAnalyser.
      
      This has been solved by using pointers to KmerSegmenter everywhere.
      f62ab84a
  10. 03 Feb, 2015 5 commits