Master

Created by: aparton

Added ambiguity flag into CL and REST VEP. Changes to ensembl-vep, ensembl-rest and public_plugins have all been made at the same time.

Requirements

• Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
• Review the contributing guidelines for this repository; remember in particular:
  • do not modify code without testing for regression
  • provide simple unit tests to test the changes
  • the PR must not fail unit testing
  • if you're adding/updating documentation of an endpoint, make sure you add/update the necessary parameters to the (template) configuration files in the ensembl-rest_private repo

Description

One or more sentences describing in detail the proposed changes.

Added in ambiguity flag for VEP

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place.

Requested by Steve T as part of VEP changes

Benefits

If applicable, describe the advantages the changes will have.

Provides ambiguity code to the user

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes.

None

Testing

Have you added/modified unit tests to test the changes?

Yes.

If so, do the tests pass/fail?

Pass, of course.

Have you run the entire test suite and no regression was detected?

Yes.

Changelog

Are you changing the functionality of an endpoint? If so, please give a one line summary for the public facing changelog.

eg. [/xenobiology/orthologs] Added allele ambiguity codes