1. 05 Jun, 2015 1 commit
  2. 21 May, 2015 1 commit
  3. 20 May, 2015 2 commits
    • Erik Garrison's avatar
      06ea37a7
    • Erik Garrison's avatar
      resolves #165 · e5c35ada
      Erik Garrison authored
      I've verified that freebayes now only works using whole-chromosome sequences.
      The anti-pattern of trying to cache little bits of the reference has been
      resolved by removing offending methods in the AlleleParser. The system should
      also run much faster.
      
      This likely affects #163, #166, #168, #170, but reporters need to test before I
      close these.
      e5c35ada
  4. 28 Apr, 2015 2 commits
  5. 23 Apr, 2015 1 commit
  6. 13 Apr, 2015 4 commits
  7. 10 Apr, 2015 1 commit
  8. 24 Mar, 2015 2 commits
  9. 11 Mar, 2015 2 commits
  10. 10 Mar, 2015 1 commit
  11. 09 Mar, 2015 2 commits
  12. 06 Mar, 2015 4 commits
  13. 05 Mar, 2015 1 commit
  14. 02 Mar, 2015 1 commit
    • Erik Garrison's avatar
      use "experimental-gls" by default · 5f1bc440
      Erik Garrison authored
      For a long time, the best way to genotype diploids using freebayes was by
      specifying --experimental-gls.  This model incorporates a lot of things into
      the genotype likelihoods (GLs) that matter, such as the effective base depth
      metric (Q = MQ * BQ) from SNPTools, and partial observation support (which
      matters for big deletions, and long haplotypes).
      
      However, bugs when handling polyploids prevented me from setting it as default.
      
      With this commit, these issues are resolved and the default is now set to what
      was previously specified by "--experimental-gls".
      
      Use --legacy-gls for old polybayes-equivalent operation.
      5f1bc440
  15. 14 Jan, 2015 5 commits
  16. 17 Dec, 2014 1 commit
  17. 15 Dec, 2014 6 commits
  18. 14 Dec, 2014 3 commits