Ga4gh-server

Alpha pre-release supporting major feature update. This release is not backwards compatible with previous releases, and requires the data files be re-imported.
- File locations are now tracked in a repo.db registry such that the files can be located anywhere. The information from the json sidecar files are also included in the database.
- Ontology terms are now imported via an OBO file instead of the old pre-packaged sequence_ontology.txt file. A sample OBO file has been added to the sample data set for the reference server.
- Added a custom landing page option for the main page of the server.
- Performance improvement for variant search when calls are set to an empty string.
- Improved server configuration including Apache configuration and robots.txt file.

Alpha pre-release supporting major feature update. This release is backwards
incompatible with previous releases, and requires a revised data directory
layout.
- Added sequence and variant annotations (which introduces a sqlite
database component)
- Added repo manager, a command line tool to manage data files and
import them into the server's data repository
- Supported searching over multiple ReadGroups, so long as they are
all in the same ReadGroupSet and all of the ReadGroups in the
ReadGroupSet are specified


data
This release contains example data that can be used with the GA4GH server for demonstration purposes. More documentation can be found [here](https://github.com/ga4gh/server/blob/master/docs/demo.rst).

This bugfix release fixes a problem introduced by upstream package changes.

Pre-release supporting major schema update. This release is backwards
incompatible with previous releases, and requires a revised data directory
layout.
- Schema version changed from v0.5 to v0.6.0a1
- Various backwards incompatible changes to the data directory layout
- Almost complete support for the API.
- Numerous code layout changes.

Alpha pre-release supporting major schema update. This release is backwards
incompatible with previous releases, and requires a revised data directory
layout.
- Schema version changed from v0.5 to v0.6.0a1
- Various backwards incompatible changes to the data directory layout
- Almost complete support for the API.
- Numerous code layout changes.

This bugfix release addresses the following issues:

455 - bugs in reads/search call (pysam calls not sanitized, wrong number of arguments to getReadAlignments)
433 - bugs in paging code for reads and variants