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Branch: master
Commits on Jun 14, 2019
  1. version changed to 1.0.0

    ngoto committed Jun 14, 2019
Commits on Sep 15, 2017
  1. Add files for packaging bio-executables gem.

    ngoto committed Sep 15, 2017
    Some files are based on "bundle gem" command.
    Some files are based on BioRuby related gems.
  2. try to use bio-old-biofetch-emulator gem

    ngoto committed Mar 18, 2015
     * bin/br_biofetch.rb: try to use bio-old-biofetch-emulator gem.
       Without bio-old-biofetch-emulator, the program exits with error
       message when default BioRuby BioFetch server is specified.
  3. Revert e29fc5fadbe0dae6528cf49637496dc2df3ec0dc

    ngoto committed Mar 18, 2015
     * bin/br_biofetch.rb: revert e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
       because the old deprecated bioruby biofetch server can be emulated
       by bio-old-biofetch-emulator gem package.
  4. remove unused $Id:$ line

    ngoto committed Nov 11, 2014
  5. Change default server to EBI Dbfetch server; remove BioRuby BioFetch …

    ngoto committed Nov 11, 2014
    …server
    
     * Change default server to EBI Dbfetch server.
     * The BioRuby BioFetch server is removed. When "-r" option (force to use
       BioRuby server) is specified, warning message is shown, and the program
       exits with code 1 (abnormal exit).
     * Usage message is also changed.
  6. When creating flatfile index, "env LC_ALL=C" is added to avoid locale…

    ngoto committed Jul 10, 2008
    … issue
    
    * In lib/bio/io/flatfile/indexer.rb and lib/bio/io/flatfile/index.rb,
      to fix a bug that invalid index is generated when LANG=en_US.UTF-8,
      when executing "/usr/bin/sort" (or sort program given by user),
      doing "/usr/bin/env LC_ALL=C" by default to avoid effects of locales.
      Note that users can specify path of env program and arguments with options.
    * In bin/br_bioflat.rb, added new option --env=/path/to/env and
      --env-arg=XXX (e.g. LC_ALL=C), corresponding to above changes.
      In addition, fixed a bug --format=XXX option was ignored.
  7. Standardize on The Ruby License

    trevor authored and ngoto committed Apr 5, 2007
  8. changed STDERR to $stderr

    ngoto committed Feb 22, 2006
  9. * license is changed to Ruby's

    ktym authored and ngoto committed Feb 9, 2006
  10. * --sort page option is now available

    ktym authored and ngoto committed Jul 11, 2005
  11. * Bio::Reference#abstract method is renamed to Bio::Reference#rd as it

    ktym authored and ngoto committed Jan 6, 2005
      produces MEDLINE abstract in RD format (part of the Ruby's documentation        format).
  12. * default format is changed to abstract

    ktym authored and ngoto committed Feb 5, 2004
  13. * PubMed search and reformatting utility

    ktym authored and ngoto committed Feb 5, 2004
  14. * --location and --dbname can also be used when --search.

    ngoto committed Aug 27, 2003
    * Added --namespace (--name) option when --search.
    * Added new action --show-namespaces to show namespaces.
  15. bioflat: changed --update option behavior

    ngoto committed Feb 28, 2003
             add --renew option (when --update)
  16. bioflat: added --update option

    ngoto committed Feb 28, 2003
  17. * bug fix, added usage

    ktym authored and ngoto committed Feb 21, 2003
  18. * added OBDA common command line interface 'bioflat_index' options:

    ktym authored and ngoto committed Feb 19, 2003
      --create, --format <genbank|embl|fasta>, --location <dir>, --dbname <name>, --indextype <bdb|flat>
  19. * removed --sort-internal option and changed --sort option

    ngoto committed Sep 16, 2002
    * added memory-efficient (but slow) sort routine
  20. * added options to bioflat for specifying primary/secondary namespaces

    ngoto committed Sep 13, 2002
    * enhanced error checks when createing index
    * inhibit some debug messages
  21. * changed to use temporary files by default

    ngoto committed Sep 11, 2002
    * added optional feature to use external sort program (e.g. /usr/bin/sort)
    * changed class hierarchy in indexer.rb
  22. * Changed internal structure

    ngoto committed Sep 4, 2002
    * Now, file format can be determined automatically. You don't need to specify it.
  23. * changed not to output debug messages by default.

    ngoto committed Aug 28, 2002
    * bioflat does not show debug messages when searching database (it still shows debug messages when creating indexes because it takes very long time).
  24. * indexer libraries are split into lib/bio/io/flatfile/indexer.rb

    ngoto committed Aug 21, 2002
    * set default action to '--search'
    * bug fix (could not make BDB index)
  25. * bio/bioflat, lib/bio/io/flatfile/index.rb, lib/bio/io/flatfile/bdb.rb

    ktym authored and ngoto committed Aug 19, 2002
      are added to support OBDA flat file indexing (by N. Goto)
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