npg_ranger project

Update

Active development is indefinitely suspended.

Introduction

This project is a contribution towards development of the streaming API under the GA4GH initiative (GA4GH Directory API and Streaming). The project has a server and a compatible command-line http client; both conform to GA4GH API

Package structure

 bin - node.js scripts, server and client
 lib - application libraries
 test - tests
 docker - scripts for deploying a server in docker containers in a cloud 
 docs - technical manuals
 docs/api - generated API (run "grunt doc" to generate)
 package.json - npm package definition
 Gruntfile.js - grunt runner specification

File merging pipeline

We are using a light version of our samtools pipeline for merging by default, but the heavy version is available in the code, located inside lib/server/model.js. This is because most of our data can work with the light pipeline, and the heavy version may be considerably more computationally taxing due to collating, fixmate, and sorting.

Related projects

• OAuth2 authorization server https://github.com/wtsi-npg/npg_sentry
• GA4GH-compatible genome browser (biodalliance) extension https://github.com/wtsi-npg/dalliance