Status

The GA4GH server is currently under active development, and several features are not yet fully functional. These mostly involve the reads API. Some missing features are:

  • Unmapped reads. We do not support searching for unmapped reads.
  • Searching over multiple ReadGroups.

For more detail on individual development issues, please see the project’s issue page.

Release Notes

0.2.0

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.

0.1.2

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

0.1.1

  • Fixes dense variants not being correctly handled by the server (#391)
  • Removes unused paths (thus they won’t confusingly show up in the HTML display at / )

0.1.0

Just bumping the version number to 0.1.0.

0.1.0b1

This is a beta pre-release of the GA4GH reference implementation. It includes

  • A fully functional client API;
  • A set of client side tools for interacting with any conformant server;
  • A partial implementation of the server API, providing supports for variants and reads from native file formats.

0.1.0a2

This is an early alpha release to allow us to test the PyPI package and the README. This is not intended for general use.