1. 12 May, 2020 1 commit
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  9. 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
  10. 26 Sep, 2016 1 commit
    • Mikaël Salson's avatar
      algo/{vidjil, core/{windows, windowExtractor}}: Add sequences of interest · 14602c22
      Mikaël Salson authored
      DNA sequences that should be found in the window (or windows that should
      be found into it) can be kept whatever their concentration is. We
      therefore extend what is already done for labelled windows.
      
      Now the sequences do not need to be the length of the window to be found
      but they can be of any length. However we require that the sequence of
      interest contains the window (or is contained in it).
      14602c22
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