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Update Bio::EnsEMBL::Exon->is_coding():

Marek Szuba requested to merge bugfix/ENSCORESW2839 into master

Created by: lairdm

  • Update documentation on required parameters
  • Throw an error if a Transcript isn't given
  • Add a test for regression

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
    • if you change the schema you must patch the test databases as well, see Updating the schema
    • the PR must not fail unit testing

Description

Updating Bio::EnsEMBL::Exon->is_coding(), documentation is out of date and parameters are properly scrutinized.

Use case

So people know how to properly use the function, and can't abuse it.

Benefits

Accurate documentation is good.

Possible Drawbacks

Code that might not properly handle an exception, but honestly, if they're not passing a transcript in already the $transcript->translation would already blow up.

Testing

Added a regression test to ensure the parameter is properly scrutinized.

If so, do the tests pass/fail?

Pass

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

Yes

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