1. 16 Mar, 2015 5 commits
  2. 14 Mar, 2015 5 commits
  3. 13 Mar, 2015 11 commits
  4. 12 Mar, 2015 14 commits
  5. 11 Mar, 2015 5 commits
    • Mathieu Giraud's avatar
      model.js, clone.js: export getPrintableSize() in .csv · e8d29139
      Mathieu Giraud authored
      These informations are not so easy to parse... but at leastthey are here.
    • Mathieu Giraud's avatar
      model.js: 'system' may be undefined · ec6d25c0
      Mathieu Giraud authored
    • Mathieu Giraud's avatar
      tests: update other tests · 9026fd39
      Mathieu Giraud authored
      As k-mers with extended nucleotides are now ignored, the count of k-mers
      in '-c germline' has slightly changed (< 0.05% variation in 'stanford-germlines.should_get').
      There are also slight changes in the number of windows found in 'stanford-w100.should_get'.
    • Mathieu Giraud's avatar
      tests: unlock tests in revcomp.should_get · 47b67b89
      Mathieu Giraud authored
      The challenging sequence isolated in 1f12079d gives now the same window
      when it is reversed-complemented. There was probably a 'N' in some IGHV germline.
    • 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.