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  6. 07 Jul, 2017 1 commit
    • Mikaël Salson's avatar
      algo/: Refactor Fasta to BioReader · 3d8ff242
      Mikaël Salson authored
      We now have an abstract class to deal with biological sequence files. This
      will allow to more easily manage different file types.
      
      This commit only reorganizes the code so that we will be able to add a BAM
      reader easily. Functionnally the code should be equivalent to its previous
      version.
      
      Some functions that were not used have been removed.
      
      The operator>> has been removed as it was only used in unit testing. This
      operator is not convenient as having the filename may be useful to reopen the
      file or to know its extension, to guess the filetype.
      
      See #2016
      3d8ff242
  7. 19 Feb, 2017 1 commit
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  21. 28 May, 2015 2 commits
    • Mathieu Giraud's avatar
      core/germline.cpp: insert D k-mers in the index · c23b5d20
      Mathieu Giraud authored
      There are sometimes common k-mers between D and V/J genes (this was at least
      the case for IGH with -t 0), and this may give badly positioned windows.
      Now all D k-mers are stored in the index, marking these k-mers as AMBIGUOUS.
      Note that it is the first time that the D germline is actually used in the KmerSegmenter.
      c23b5d20
    • Mikaël Salson's avatar
      algo/: Remove delta_max, use delta_min only in FineSegmenter. · d567545c
      Mikaël Salson authored
      delta_max is now useless. It was use to make sure we didn't segment
      something not robust enough. Now we use the e-value, which is a much
      trustable value.
      
      delta_min is useless to the KmerSegmenter (we can't have overlaps
      with the first_max, last_max algorithms).
      But it can still be useful to FineSegmenter, that's why we keep it.
      d567545c