ga4gh / ga4gh/hackathon2016

Implement an evaluation framework for software that manipulates HGVS-formatted variants

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Description

IMPORTANT: This hackathon will now be held at the Marriott, near the Vancouver Convention Center. See http://www.ga4gh.org/#/hackathon2016 for details.
## Background

HGVS is a syntax and set of recommendations used to represent sequence variants. The guidelines are broad and complex, and packages that implement these guidelines may not implement all features or may miss critical cases. This leads to uncertainty among users about which packages to use for particular purposes. The goal of the hgvs-eval project is to provide an objective framework by which HGVS tools may be assessed. It is envisioned that the primary user-visible product will be a web page that facilitates comparing packages (and package versions) on evaluation suite results.
## Major tasks

Specific tasks for this project are:
- Define REST interface for manipulating HGVS variants.
- Define and implement an initial set of tests by which packages will be assessed.
- Implement tests. Implementation will enable both language-agnostic unit tests as well as REST-based evaluation.
- Implement REST interface for one package (https://bitbucket.org/biocommons/hgvs/).
- Implement a test database and rudimentary web interface that summarizes results.
- Document REST interface using swagger or RAML, sufficient to enable package owners to implement a REST interface using their tools.

Note: A REST interface, tests, and design considerations are provided in this draft proposal, which will be refined prior to the HackSeq event.
## Ideal candidates

First, you're all ideal. :smile:

The implementation will be in Python, so all contributors should have good Python skills. In addition, applicants should have experience with at least a few of the following: Python unit testing, REST interface design, HGVS variant nomenclature, simple web interfaces.

Participants: @cchng @dandanxu @jpdna @davecap @nicoleruiz (remote) @reece

Project Lead: Reece Hart / @reece / Industry Professional / Invitae

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