1. 18 Jun, 2018 4 commits
    • Mikaël Salson's avatar
    • Mikaël Salson's avatar
      testSegment.cpp: Not ambiguous anymore · acea9c6e
      Mikaël Salson authored
      The test was classified as ambigious but it probably should not have been. The
      fact of having not enough Vs should have classified the read as UNSEG_ONLY_J.
      
      Now the overlapping k-mers where we maximize the score (with the 'before'
      affects at the left and the 'after' affects at the right) are ignored. This
      therefore gives us the UNSEG_ONLY_J.
      
      The previous UNSEG_AMBIGUOUS was due to the fact that some 'after' affects
      (the Js overlapping the end of Vs) were counted left affects and that there
      was too many left Js.
      
      Thus we now have 4 UNSEG_ONLY_J sequences and 1 UNSEG_AMBIGUOUS.  As the
      sequence whose unsegmentation cause changes is 33nt long, the average length
      changes accordingly.
      
      See #3296
      acea9c6e
    • Mikaël Salson's avatar
      core/affectanalyser.cpp: Don't count affects that are on a plateau of max values · c0271f69
      Mikaël Salson authored
      When they were counted this biased the counter of before affects on the left part thus
      leading to unjustified UNSEG_AMBIGUOUS.
      
      When we are on a plateau and when affectations[i] is defined this means we have overlapping k-mers
      thus we don't count those k-mers as left affects (are they left or right? we are actually **on**
      the maximum, it is hard to tell).
      
      However if we happen to encounter a higher maximum those ignored values are then reaffected to the left
      counters.
      
      Fix #3296
      c0271f69
    • Mikaël Salson's avatar
      testAffectAnalyzer: Test two cases where we have overlapping before/after affects · 4e2cc265
      Mikaël Salson authored
      This causes the heuristic not to be symmetric because and having
      an undesired behaviour.
      In such a case we have a plateau with the maximal value. This plateau
      is reached when we have the overlapping V/J. But in this case the J
      affects are counted « left » which then prevents the heuristic from
      segmenting the sequence as the number of after affects (the Js)
      on the left part is too high.
      
      Therefore this has to be changed to that the overlapping affects
      are not counted anymore as left or right.
      
      See #3296
      4e2cc265
  2. 15 Jun, 2018 19 commits
  3. 14 Jun, 2018 4 commits
  4. 13 Jun, 2018 13 commits