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GA4GH Client Implementation

ga4gh-client is a package that contains the client functionality of the ga4gh package.

See the documentation for the ga4gh package on its readthedocs page.

Contents:

Python Client Library

This is the GA4GH client API library. This is a convenient wrapper for the low-level HTTP GA4GH API, and abstracts away network centric details such as paging. The methods and types used by the client library are defined by the GA4GH schema.

Warning

This client API should be considered early alpha quality, and may change in arbitrary ways.

Todo

A full description of this API and links to a tutorial on how to use it, as well as a quickstart showing the basic usage.

Types

Todo

Add links to the upstream documentation for the GA4GH types.

Client API

Todo

Add overview documentation for the client API.

Release Notes

0.6.0a10

Features:

  • Added support for BigWig files in a new Continuous Data object (#63) New endpoints and message types include:
  • POST /continuoussets/search
  • GET /continuoussets/{id}
  • POST /continuous/search
  • Continuous (new)
  • ContinuousSet (new)
  • Add ability to list and join peer server networks (#60) New endpoints and message types include:
  • POST /peers/list
  • POST /peers/announce
  • GET /info
  • ListPeersResponse (new)
  • Peer (new)
  • AnnouncePeerResponse (new)
  • GetInfoResponse (new)
  • Remove feature_id from ExpressionLevel and add ability to search by the Name field (#67) Impacts
  • POST /expressionlevels/search
  • GET /expressionlevels/{id}
  • Replaced info fields with rich type Attributes fields (#46) Impacts the following message types:
  • TranscriptEffect
  • VariantAnnotation
  • Individual
  • Biosample
  • Experiment (new)
  • Analysis (new)
  • Dataset
  • ReadGroup
  • ReadGroupSet
  • ReadAlignment
  • Reference
  • ReferenceSet
  • RnaQuantificationSet
  • RnaQuantification
  • ExpressionLevel
  • Feature
  • VariantSetMetadata
  • CallSet
  • Call
  • Variant
  • Replace NCBI taxon ID integer with ontology term. Impacts the following message types:
  • Reference
  • ReferenceSet
  • Changed ontology term “id” to “term_id” (#48) Impacts the following message types:
  • OntologyTerm

Documentation:

  • Created a basic Info page for the Pypi repository (#68)

0.6.0a9.post2

Bugfix release which uses the new release process.

0.6.0a9.post1

Bugfix release which fixes the following issues:

  • wrong attributes on RnaQuantification (#53)
  • wrong attributes on ExpressionLevels (#51)

0.6.0a9

A new versioning scheme has been introduced that will make it easy to tell which version of the client to use against a protocol version!

  • Calls are now returned as ListValues and can be int32, empty, or strings

    to cover the case when a VCF call states no call was made.

  • Refactor “BioSample” to “Biosample”.

  • Switch to stable protobuf version (3.1).

  • Improve generated documentation.

  • Add authorization via headers.

0.0.4

0.0.3

Add hierachical namespace

0.0.2

Release using new ga4gh packages, ga4gh-common and ga4gh-schemas

0.0.1

Initial release