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Investigate and improve hgvs performance#


Difficulty Expected Duration Possible Mentors
Medium 175h @reece


The goal of this project is to collect profiling data for the hgvs package, identify and triage opportunities for improvement, and to undertake some of those improvements.

Community Outcomes#

Improving the performance of hgvs will create a better experience for users and may enable new uses, such as on-the-fly variant translation in user interfaces.

Expected Results / Deliverables#

  • Collect and present performance profiling data for common operations in hgvs
  • Discuss opportunities for improvement with the community in order to prioritize performance improvements
  • Implement several performance improvements and collect data to demonstrate the value

Required and Desired Skills#

  • Deep python experience, including performance profiling
  • Ability to visualize code paths and identify areas of improvement

Benefits to Intern#

The intern will gain familiarity with the processing of sequence variants and refine his/her experience with performance improvements in code.

How to apply#

Students applying to this project should briefly describe their vision for this project, highlight their existing skills and the skills they would need to learn, and estimate an implementation timeline.