[Bioperl-guts-l] [bioperl/bioperl-live] 532dcf: Worked around changes in memory adapter without ab...

noreply at github.com noreply at github.com
Wed Mar 9 22:20:45 EST 2011


Branch: refs/heads/master
Home:   https://github.com/bioperl/bioperl-live

Commit: 532dcfc730e0e77e902cf1a15d6c61fe6e074a07
    https://github.com/bioperl/bioperl-live/commit/532dcfc730e0e77e902cf1a15d6c61fe6e074a07
Author: Lincoln Stein <lincoln.stein at gmail.com>
Date:   2011-03-09 (Wed, 09 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm
  M Bio/DB/SeqFeature/Store/DBI/SQLite.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M Bio/DB/SeqFeature/Store/GFF3Loader.pm
  M Bio/DB/SeqFeature/Store/berkeleydb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb3.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
Worked around changes in memory adapter without abolishing the features
that Florent added to the memory adapter. Please revisit the decision to
allow arbitrary primary_ids in features that can be stored to the database.


Commit: 455ed6fe184610a8b75dc49b831ff012f67a15c3
    https://github.com/bioperl/bioperl-live/commit/455ed6fe184610a8b75dc49b831ff012f67a15c3
Author: Lincoln Stein <lincoln.stein at gmail.com>
Date:   2011-03-09 (Wed, 09 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/berkeleydb3.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
improved performance of SQLite and mysql adaptors when loading many DNA sequences; fixed berkeleydb3 adaptor to return correct result from get_features_by_type() when called with a primary_tag and no source


Commit: 1c2cf247fd97c4d536054b2136282af69644e4e8
    https://github.com/bioperl/bioperl-live/commit/1c2cf247fd97c4d536054b2136282af69644e4e8
Author: Lincoln Stein <lincoln.stein at gmail.com>
Date:   2011-03-09 (Wed, 09 Mar 2011)

Changed paths:
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm
  M Bio/DB/SeqFeature/Store/DBI/SQLite.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M Bio/DB/SeqFeature/Store/berkeleydb.pm
  M Bio/DB/SeqFeature/Store/berkeleydb3.pm
  M t/LocalDB/SeqFeature.t

Log Message:
-----------
fixed up berkeleydb adaptor to pass new set of regression tests


Compare: https://github.com/bioperl/bioperl-live/compare/2de6af1...1c2cf24


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