Merging of unified-design with master branches
Created by: tgrego
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 Ensembl contributing guidelines; 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
Description
This brings the feature/unified-design branch into master. No conflicts exist, and all existing tests are passing (which is the essential functionality for web usage). RDF support (both reading and writing) is included, so production does not have to checkout feature/unified-design branch to use it. New writer design is in place, and support for writing GTF, GFF3 and VCF4 (in addition to RDF as mentioned before). Writing of other filetypes (such as FASTA and BED) is not possible as that is not yet implemented. Implementation and tests for missing writers is required! Current master branch does not have writer tests, and ad hoc testing has shown it to be non-functional (thus no functionality is being lost with the merge).
Benefits
RDF support and new writer design. Unified master branch for a new round of development and feature implementation!
Possible Drawbacks
Old writer design disappears so code that was writing files will not work anymore. However, I could not find code that was writing files using that old design, and it does not seem to be working anyways...
Testing
Have you added/modified unit tests to test the changes? yes
If so, do the tests pass/fail? pass
Have you run the entire test suite and no regression was detected? yes