1. 13 Sep, 2016 1 commit
  2. 24 Jun, 2016 4 commits
  3. 23 Jun, 2016 5 commits
  4. 22 Jun, 2016 6 commits
  5. 15 Jun, 2016 4 commits
  6. 14 Jun, 2016 5 commits
    • Vermaat's avatar
      Merge pull request #403 from mutalyzer/snp-convert-ncbi · 680f8d16
      Vermaat authored
      Move dbSNP query to ncbi module
      680f8d16
    • Vermaat's avatar
      Move dbSNP query to ncbi module · 473bf878
      Vermaat authored
      This removes 25% of the code from the Retriever module which didn't
      really belong there in the first place.
      
      No output object is used anymore, a simple exception is thrown on
      connection errors. We also removed the auto retry around the Entrez call
      which I think didn't fix a problem that's ours to fix and added a lot of
      complexity.
      473bf878
    • Vermaat's avatar
      Improve error handling in NCBI Entrez calls · 989e50d2
      Vermaat authored
      989e50d2
    • Vermaat's avatar
      Merge pull request #402 from mutalyzer/ref-acc-no-version · a60fb45a
      Vermaat authored
      Revert adding Reference.version column
      a60fb45a
    • Vermaat's avatar
      Revert adding Reference.version column · 6e5a04ef
      Vermaat authored
      While working on this, I came to the conclusion it's not a good idea to
      split accession and version. It introduces a lot of complexity for
      little benefit.
      
      In general, Mutalyzer always sees 'accession.version' as the identifier
      of the reference and because we always want exact identifiers, there is
      little need for accession numbers without version.
      
      The most obvious use case I see for a split is that we can easily query
      available references with a certain accession, not taking version into
      account, as a way to inform the user when a specific reference
      identifier was not found. But I guess we better have this use case as
      the exception, and make our life easier for the rest.
      
      So I guess I'm aborting this for now. Addition of the `version` column
      has already landed in the master branch, but this is easy to roll
      back. The original column has not yet been touched in master.
      6e5a04ef
  7. 13 Jun, 2016 3 commits
  8. 12 Jun, 2016 4 commits
  9. 10 Jun, 2016 2 commits
  10. 09 Jun, 2016 6 commits