1. 16 Dec, 2014 1 commit
  2. 03 Dec, 2014 1 commit
    • Mathieu Giraud's avatar
      core/segment.{h,cpp}: both V and J kmers must be above DETECT_THRESHOLD to... · a8df78ec
      Mathieu Giraud authored
      core/segment.{h,cpp}: both V and J kmers must be above DETECT_THRESHOLD to flag the germline as 'detected'
      
      This reverts the idea of 41b4f071, but still uses a 'detected' flag.
      This flag tells us whether we should continue to the remaining germlines.
      In the case of incomplete rearrangements, we certainly want to continue even if we have
      many V or many J (but now both of them).
      Tests d2a0dbd5 are now passing.
      
      Note that we don't run this test when strand == 2, this should be changed.
      a8df78ec
  3. 22 Nov, 2014 1 commit
    • Mathieu Giraud's avatar
      core/segment.cpp: UNSEG_AMBIGUOUS of the previous commits becomes a 'detected' flag · 41b4f071
      Mathieu Giraud authored
      ABIGUOUS_THRESHOLD becomes DETECTED_THRESHOLD, such reads are flag 'detected'
      
      This is cleaner: on one side we have the cause of unsegmentation, on the other we have the
      flag 'detected' if there were enough V+J (now total V+J, we don't need to have both V and J).
      Currently, the flag can be set when SEG_+/, TOO_FEW_V/J, or DELTA_MIN/MAX (but not STRAND).
      
      We do not continue to the remaining germlines when 'detected' or STRAND.
      41b4f071
  4. 21 Nov, 2014 1 commit
  5. 01 Nov, 2014 1 commit
  6. 20 Oct, 2014 1 commit
  7. 14 Oct, 2014 1 commit
  8. 01 Oct, 2014 3 commits
  9. 08 Aug, 2014 1 commit
  10. 07 Jul, 2014 2 commits
  11. 03 Jul, 2014 1 commit
  12. 16 May, 2014 1 commit
  13. 14 Apr, 2014 1 commit
  14. 27 Mar, 2014 1 commit
  15. 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
  16. 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
  17. 26 Apr, 2013 1 commit