Skip to content


Subversion checkout URL

You can clone with
Download ZIP

Comparing changes

Choose two branches to see what’s changed or to start a new pull request. If you need to, you can also compare across forks.

Open a pull request

Create a new pull request by comparing changes across two branches. If you need to, you can also compare across forks.
Commits on Jul 29, 2010
@rbuels rbuels little branch for a postgres version of the gbrowse_syn multiple alig…
…nments loader
@rbuels rbuels more-standard-sql version of the gbrowse_syn multiple alignment loade…
…r. this works in postgres. this might also work in mysql, but it needs testing
Commits on Aug 05, 2011
@rbuels rbuels first crack at porting the to …
…postgres also
Commits on Aug 08, 2011
@dbolser dbolser sligntly improved the documentation and changed some formatting (you …
…may want to diff with --ignore-whitespace)
@dbolser dbolser rewrote to use IDENTICAL copie…
…s of the subroutines used in The next step is to split these subs out, or merge the two scripts.
@dbolser dbolser debugging, enable keys was from mysql, removed for pg 746b980
@rbuels rbuels Merge pull request #7 from dbolser/postgres_gbrowse_syn_load_alignmen…

Postgres gbrowse syn load alignments msa
Commits on Aug 11, 2011
@rbuels rbuels Merge branch 'postgres_gbrowse_syn_load_alignments_msa' into syn_2x_p…
@rbuels rbuels moved Bio::DB::Synteny* modules to a Bio::DB::Synteny::Store namespace 8d1ee48
@rbuels rbuels clean up some queries 29bb430
@rbuels rbuels get rid of fatalstobrowser uses, these should not be committed in pro…
…duction code
Commits on Aug 15, 2011
@rbuels rbuels big refactor of gbsyn database code into a cross-database system, Bio…
…::DB::Synteny::Store, similar in structure to Bio::DB::SeqFeature::Store
Commits on Aug 16, 2011
@rbuels rbuels tweak synteny db backend dsn-munging f4cb694
@rbuels rbuels fix SQLite synteny backend table dropping 56cb418
@rbuels rbuels fix synteny Pg backend deploy c0762e5
@rbuels rbuels fill in synteny mysql backend deployment 58b2f4e
@rbuels rbuels refactored into Bio::DB::Synte…
…ny::Store::Loader::Tabular, refactored Loaders to have a common superclass. no tests for tabular loader yet, need to get some test data
@rbuels rbuels add test for gbsyn tabular loader 5554604
@rbuels rbuels bugfix to gbsyn tabular loader 1ee44fb
@rbuels rbuels add some POD 9a0dc72
@rbuels rbuels wrap syn_store loads in transactions for better performance. non-tran…
…sactional DBI backends will ignore the AutoCommit settings, I think
@rbuels rbuels warning squash 29e92da
@rbuels rbuels import missing binning function in syn dbi superclass 7b772f5
@rbuels rbuels make the gbsyn viewing code use the new synteny backend d779891
@rbuels rbuels Merge branch 'syn_2x_postgres' into syn_2x
Something went wrong with that request. Please try again.