1. 13 Jan, 2017 16 commits
  2. 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
  3. 27 Jun, 2016 1 commit
  4. 20 Jun, 2016 1 commit
  5. 18 Dec, 2015 1 commit
  6. 15 Jun, 2015 4 commits
  7. 12 Jun, 2015 1 commit
  8. 04 Jun, 2015 1 commit
  9. 21 May, 2015 1 commit
  10. 20 May, 2015 1 commit
  11. 15 May, 2015 1 commit
  12. 08 May, 2015 2 commits
  13. 29 Apr, 2015 1 commit
  14. 06 Apr, 2015 1 commit
  15. 01 Apr, 2015 2 commits
  16. 19 Mar, 2015 1 commit
  17. 11 Mar, 2015 1 commit
    • Mathieu Giraud's avatar
      core/kmerstore.h: ignore all k-mers with extended nucleotides when updating index · b0e3045d
      Mathieu Giraud authored
      There are some 'N' and other extended nucleotides in the germline sequences.
      As we store in the indexes both the k-mers and their reverse complement, and as
      we handle extended nucleotides almost randomly (see tools:nuc_to_int()),
      we may have slight differences when analyzing some reads and their reverse complement.
      Ignoring such k-mers allow thus to be more deterministic, getting the same
      results on a (pure ACGT) read and its reverse complement.
      
      Another option (harder to implement) could be to add several k-mers in the index,
      but this would decrease the effective weight of the seed.
      
      Note that we should also improve the analysis of reads that includes extended nucleotides.
      b0e3045d
  18. 04 Nov, 2014 1 commit