1. 23 Jul, 2018 1 commit
  2. 13 Jun, 2018 1 commit
  3. 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
  4. 14 Mar, 2017 1 commit
  5. 13 Jan, 2017 20 commits
  6. 28 Sep, 2016 3 commits
    • Mikaël Salson's avatar
      kmerstore.h: satisfy clang · 01e7f4b4
      Mikaël Salson authored
      For an unknown reason, Clang complained about the line:
      seed = IKmerStore<T>::seed
      because “error: no viable overloaded '='”
      It seemed to interpret one of the variable as const (which is not)
      as it indicated:
      /usr/bin/../lib/gcc/x86_64-linux-gnu/6.1.1/../../../../include/c++/6.1.1/bits/basic_string.h:565:7: note: candidate function not viable: 'this' argument has type 'const string' (aka 'const basic_string<char>'),
            but method is not marked const
      
      The solution was to use a local variable. Clang was happy, but I don't
      see what really makes the difference.
      01e7f4b4
    • Mikaël Salson's avatar
      kmerstore.h: Inserting with a seed. · 83ff2886
      Mikaël Salson authored
      Let the possibility to provide a seed when inserting in a
      KmerStore. This will be particularly suitable with an index having
      different seeds depending on the sequences.
      83ff2886
    • Mikaël Salson's avatar
      IKmerStore: getResults() depending on seed · daffb14f
      Mikaël Salson authored
      We can provide a seed to the getResults() method to have results
      depending on a seed. Therefore multiple seeds can be used to index.
      daffb14f
  7. 27 Jun, 2016 1 commit
  8. 20 Jun, 2016 1 commit
  9. 18 Dec, 2015 1 commit
  10. 15 Jun, 2015 4 commits
  11. 12 Jun, 2015 1 commit
  12. 04 Jun, 2015 1 commit
  13. 21 May, 2015 1 commit
  14. 20 May, 2015 1 commit
  15. 15 May, 2015 1 commit
  16. 08 May, 2015 1 commit