1. 01 Apr, 2021 1 commit
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  12. 23 Sep, 2016 1 commit
    • Mikaël Salson's avatar
      vidjil.cpp (tests and doc): -t options defaults again to 0 · cd292aa0
      Mikaël Salson authored
      This reverts bf2f96fe and d317535b.
      
      After more than one year experience with -t 100 we realised that trimming leads to:
      – missing special cases where the V gene is heavily trimmed
      – giving bad unsegmentation causes: UNSEG only J appeared in cases where it didn't make sense
        those unsegmentation causes were replaced by UNSEG only V when changing -t to 0 (that also let us think that we could miss some V genes)
      
      However -t 0 does have a drawback that should be addressed. It is more likely to have
      spurious hits of V genes in the N-region (particularly with VDJ recombinations
      where the N-region is longer). Those spurious hits tend to shift the window towards
      the J gene.
      
      In the tests the modifications are due either to slight changes in number of windows
      (a small increase due to the previous reason) or to an increase in unsegmentation
      with really large windows (since windows are shifted we may not have
      enough space left to put a window).
      cd292aa0
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  25. 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
  26. 07 Oct, 2013 1 commit
    • Mikaël Salson's avatar
      Vidjil: release 2013.10 · 2cbd3725
      Mikaël Salson authored
      	* Better heuristic, segments more reads (core/segment.cpp)
      	* Better and faster selection of representative read (vidjil.cpp, core/read_chooser.cpp)
      	* Better display of reason of non-segmenting reads
      	* New normalization against a standard (-Z) (core/labels.cpp)
      	* New experimental lazy_msa multiple aligner
      	* New .json output
      	* New unit tests
      	* Bugs closed
      2cbd3725