This project is mirrored from https://:*****@github.com/Ensembl/ensembl-io.git. Pull mirroring updated .
  1. 28 Jun, 2017 1 commit
    • Zhicheng Liu's avatar
      Rework on how Bio::DB::HTS is used in HTSAdaptor · 73e743ef
      Zhicheng Liu authored
      The Bio::DB::HTS object and other relatedHTS objects will be created
      only once within a single HTSAdaptor. They will have only one copy and
      be stored in $self->{_cache}->{_htsobj_handle}. Every use of HTS objects
      should through this copy.
      
      Also remove "close" calls to the HTS objects as these objects will
      handle their resources properly when exiting. The DESTROY methods to
      these objects has been added in
      https://github.com/Ensembl/Bio-DB-HTS/pull/50
      which will release the resources where needed.
      
      This will provide a uniform interface to HTS objects, making it more
      consistent. It prevents from creating multiple objects for the same
      file and hence more resouces efficient too.
      
      Also rename some variables to make them consistent throughout.
      
      Related to ENSEMBL-5035.
      73e743ef
  2. 27 Jun, 2017 2 commits
  3. 13 Jun, 2017 4 commits
  4. 12 Jun, 2017 2 commits
  5. 19 May, 2017 1 commit
  6. 14 Mar, 2017 2 commits
  7. 19 Jan, 2017 1 commit
  8. 17 Jan, 2017 1 commit
  9. 12 Jan, 2017 1 commit
  10. 04 Jan, 2017 5 commits
  11. 22 Dec, 2016 2 commits
  12. 13 Dec, 2016 1 commit
  13. 17 Nov, 2016 1 commit
  14. 11 Nov, 2016 1 commit
  15. 21 Oct, 2016 1 commit
  16. 10 Oct, 2016 2 commits
  17. 06 Oct, 2016 1 commit
  18. 05 Oct, 2016 1 commit
  19. 03 Oct, 2016 1 commit
  20. 30 Sep, 2016 1 commit
  21. 14 Sep, 2016 1 commit
  22. 13 Sep, 2016 1 commit
    • William McLaren's avatar
      Modify how TextParser responds to failed read · e5fd6b6f
      William McLaren authored
      On some filehandles eof() does not correctly report the end of the
      file. To this end I've changed the code so that confess() is only
      called if the _first_ call to read from the filehandle fails.
      
      A fail after one or more successful reads is then treated as
      reaching eof(). After reaching eof() in this way, a further call
      to read_block() will then trigger an error and confess().
      e5fd6b6f
  23. 05 Sep, 2016 2 commits
  24. 22 Aug, 2016 2 commits
  25. 16 Aug, 2016 1 commit
  26. 11 Aug, 2016 1 commit