GA4GH Reference Implementation

This is a prototype for the GA4GH reference client and server applications. It is under heavy development, and many aspects of the layout and APIs will change as requirements are better understood. If you would like to help, please check out our list of issues!

Our aims for this implementation are:

Simplicity/clarity

The main goal of this implementation is to provide an easy to understand and maintain implementation of the GA4GH API. Design choices are driven by the goal of making the code as easy to understand as possible, with performance being of secondary importance. With that being said, it should be possible to provide a functional implementation that is useful in many cases where the extremes of scale are not important.

Portability

The code is written in Python for maximum portability, and it should be possible to run on any modern computer/operating system (Windows compatibility should be possible, although this has not been tested). Our coding guidelines specify using a subset of Python 3 which is backwards compatible with Python 2 following the current best practices. The project currently does not yet support Python 3, as support for it is lacking in several packages that we depend on. However, our eventual goal is to support both Python 2 and 3.

Ease of use

The code follows the Python Packaging User Guide. Specifically, pip is used to handle python package dependencies (see below for details). This allows for easy installation of the ga4gh reference code across a range of operating systems.

Configuration file and data hierarchy

The GA4GH reference server is a Flask application and uses the standard Flask configuration file mechanisms. An example configuration file might look like:

DATA_SOURCE = "/path/to/data/root"
# TODO other example config

Data is input to the GA4GH server as a directory hierarchy, in which the structure of data to be served is represented by the filesystem. For now, we support only one dataset, but this will be generalised to multiple datasets in later releases. An example data layout might be:

ga4gh-data/
    /variants/
        variantSet1/
            chr1.vcf.gz
            chr1.vcf.gz.tbi
            chr2.vcf.gz
            chr2.vcf.gz.tbi
            # More VCFs
        variantSet2/
            chr1.bcf
            chr1.bcf.csi
            chr2.bcf
            chr2.bcf.csi
            # More VCFs
    /reads/
        readGroupSet1
            # TODO fill in details for read data.