Changelog

5.0.0 2014-11-14

New filter option --genes-to-keep Allows filtering by Entrez gene ID to keep only those genes specified.
Added caching options which may significantly increase performance at the expense of memory - see application.properties.
Changed 'username' in application.properties to 'dbuser' to prevent the current user's username from being used to authenticate against the PostgreSQL database on Windows.
Added missing full-analysis option to test and example.settings
Updated external dependencies
Lots of under the hood changes and increased test coverage in exomiser-core.
Focused on improving test coverage of the Factory and DAO packages in particular.
API changes:
- FrequencyDao and PathogenicityDao are now interfaces implemented by DefaultFrequencyDao and DefaultPathogenicityDao
- New PedigreeFactory split out of SampleDataFactory
- GeneFactory is no longer a static class
- VariantEvaluationDataFactory renamed to VariantVariantEvaluationDataService
- Removed unused constructors from SampleData
- Added getEntrezGeneID method to VariantEvaluation to make API more consistent and lessen direct dependency on Jannovar Variant in the rest of the code.
- Removed unused PhredScore class
- FilterFactory now returns more specific Filter types - VariantFilter and GeneFilter from the relevant methods