…annotations from phenotype.hpoa

Update application.properties and ResourceConfigurationProperties to remove unused fields.
Update DiseaseInheritanceCacheReader and DiseasePhenotypeReader to parse phenotype.hpoa file
Update DiseaseResourceConfig to use hpoa resource

…acking frequency information.

Update Acgs2020Classifier and Acmg2015Classifier to allow for PVS1 and PM2_Supporting are sufficient to trigger LIKELY_PATHOGENIC
Change for issue #514 update AcmgEvidence to fit a Bayesian points-based system
Add new Acmg2020PointsBasedClassifier to classify AcmgEvidence based on points

…opulation frequency filtering

Add new FrequencySource.NON_FOUNDER_POPS to exclude FIN, ASJ, OTH ExAC and gnomAD populations.
Update Acmg2015EvidenceAssigner to implement updated guidelines from ClinGen SVI for BA1 and PM2 see issue #513 for details

…om presets and examples.

…MG_DISEASE_NAME` INFO sub-field

Update JannovarProtoConverter to handle new Alignment requirement
Add tests to check handling of reading pre and post update Jannovar data
Update JannovarVariantAnnotatorTest to check correct annotation of mitochondrial variants requiring use of the mitochondrial-specific encodings in the codon table

…requency, if present,