├── .gitbook.yaml ├── .github └── workflows │ ├── develop.yml │ ├── manual-delete-docker.yml │ ├── manual-test.yml │ ├── pull-request-approved.yml │ ├── pull-request-merge.yml │ ├── r-release.yml │ ├── release.yml │ ├── reusable-delete-docker.yml │ ├── scripts │ ├── get-xetabase-branch.sh │ └── get_same_branch.sh │ ├── task.yml │ └── test-analysis.yml ├── .gitignore ├── Jenkinsfile ├── LICENSE ├── cellbase-app ├── app │ ├── clients │ │ ├── java_client_generator.py │ │ ├── js_client_generator.py │ │ ├── python_client_generator.py │ │ ├── r_client_generator.py │ │ └── rest_client_generator.py │ ├── cloud │ │ ├── docker │ │ │ ├── README.md │ │ │ ├── cellbase-base │ │ │ │ └── Dockerfile │ │ │ ├── cellbase-builder │ │ │ │ └── Dockerfile │ │ │ ├── cellbase-python │ │ │ │ └── Dockerfile │ │ │ ├── cellbase-rest │ │ │ │ └── Dockerfile │ │ │ └── docker-build.py │ │ └── kubernetes │ │ │ ├── charts │ │ │ ├── cellbase │ │ │ │ ├── .helmignore │ │ │ │ ├── Chart.yaml │ │ │ │ ├── NOTES.txt │ │ │ │ ├── templates │ │ │ │ │ ├── NOTES.txt │ │ │ │ │ ├── _helpers.tpl │ │ │ │ │ ├── azurefile │ │ │ │ │ │ ├── azure-file-secret.yml │ │ │ │ │ │ └── pv-azurefiles.yaml │ │ │ │ │ ├── cert-issuer │ │ │ │ │ │ ├── private-issuer.yaml │ │ │ │ │ │ └── public-issuer.yaml │ │ │ │ │ ├── configmap.yaml │ │ │ │ │ ├── load-job.yaml │ │ │ │ │ ├── mongodb │ │ │ │ │ │ ├── mongodb-cert.yaml │ │ │ │ │ │ ├── mongodb-password-secret.yaml │ │ │ │ │ │ ├── mongodb-replicaset.yaml │ │ │ │ │ │ └── mongodb-roles.yaml │ │ │ │ │ ├── pvc.yaml │ │ │ │ │ ├── rest-deployment.yaml │ │ │ │ │ ├── rest-ingress.yaml │ │ │ │ │ ├── rest-network-policy.yaml │ │ │ │ │ ├── rest-service.yaml │ │ │ │ │ ├── rest-serviceaccount.yaml │ │ │ │ │ ├── validate.tpl │ │ │ │ │ ├── worker-deployment.yaml │ │ │ │ │ └── worker-serviceaccount.yaml │ │ │ │ └── values.yaml │ │ │ ├── cert-manager │ │ │ │ └── values.yaml │ │ │ ├── mongodb-operator │ │ │ │ └── values.yaml │ │ │ └── nginx │ │ │ │ └── values.yaml │ │ │ └── deploy.sh │ ├── conf │ │ └── cellbase-env.sh │ ├── example │ │ ├── 5000_variants.vcf.gz │ │ ├── BasicTest.Json │ │ ├── BasicTest.gvf │ │ ├── Escherichia coli.owl │ │ ├── Homo_sapiens_incl_consequences_1000.Json │ │ └── Homo_sapiens_incl_consequences_1000.gvf │ ├── mongodb-scripts │ │ ├── add_database_roles_mongo.js │ │ ├── create-biouser.js │ │ └── grant-users.js │ ├── monitor │ │ └── README.md │ └── scripts │ │ ├── bigWigToBedGraph │ │ ├── clinvar │ │ └── clinvar_spliter.pl │ │ ├── cosmic │ │ └── cosmic_mutations.sh │ │ ├── ensembl-scripts │ │ ├── DB_CONFIG.pm │ │ ├── gene_extra_info.pl │ │ ├── genome_info.pl │ │ ├── protein_function_prediction_matrices.pl │ │ ├── registry.conf │ │ ├── transcript_seqs.pl │ │ ├── variation.pl │ │ └── variation_simulation.pl │ │ ├── gnomad │ │ └── mitochondrial │ │ │ ├── README.md │ │ │ ├── gnomad_mt.py │ │ │ └── opencga_gnomad_mt.sh │ │ ├── gnomad_mt_prepare.py │ │ ├── obsolete │ │ ├── cellbase-builder.py │ │ ├── cellbase-installer.py │ │ ├── cellbase-load.py │ │ ├── gene-chunkIds.js │ │ ├── genome-fetcher │ │ │ ├── CHECKSUMS │ │ │ ├── DB_CONFIG.pm │ │ │ ├── genome-fetcher.py │ │ │ ├── species.json │ │ │ ├── species_info.json │ │ │ └── species_info.txt │ │ ├── genome_info.pl │ │ ├── idmapping_to_xrefs.py │ │ └── variation-chunkIds.js │ │ ├── protein │ │ └── uniprot_spliter.pl │ │ └── pycellbase │ │ ├── README.md │ │ ├── gene_query.py │ │ └── utils │ │ └── canonical.py ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── opencb │ │ └── cellbase │ │ └── app │ │ └── cli │ │ ├── CliOptionsParser.java │ │ ├── CommandExecutor.java │ │ ├── admin │ │ ├── AdminCliOptionsParser.java │ │ ├── AdminMain.java │ │ └── executors │ │ │ ├── ApiKeyCommandExecutor.java │ │ │ ├── BuildCommandExecutor.java │ │ │ ├── CustomiseCommandExecutor.java │ │ │ ├── DataReleaseCommandExecutor.java │ │ │ ├── DownloadCommandExecutor.java │ │ │ ├── ExportCommandExecutor.java │ │ │ ├── IndexCommandExecutor.java │ │ │ ├── InstallCommandExecutor.java │ │ │ ├── LoadCommandExecutor.java │ │ │ ├── ServerCommandExecutor.java │ │ │ ├── ValidationCommandExecutor.java │ │ │ └── validation │ │ │ ├── TranscriptConsequence.java │ │ │ └── VEPVariant.java │ │ ├── main │ │ ├── CellBaseCliOptionsParser.java │ │ ├── CellBaseMain.java │ │ ├── annotation │ │ │ ├── BenchmarkDataWriter.java │ │ │ ├── BenchmarkTask.java │ │ │ ├── CellBaseLocalVariantAnnotator.java │ │ │ ├── CellBaseWSVariantAnnotator.java │ │ │ ├── JsonStringAnnotatorTask.java │ │ │ ├── PopulationFrequenciesAnnotator.java │ │ │ ├── SequenceOntologyTermComparisonObject.java │ │ │ ├── VariantAnnotationDiff.java │ │ │ ├── VariantAnnotatorTask.java │ │ │ ├── VariationDataReader.java │ │ │ ├── VcfStringAnnotatorTask.java │ │ │ ├── VcfVariantAnnotator.java │ │ │ └── indexers │ │ │ │ ├── CustomAnnotationVariantIndexer.java │ │ │ │ ├── PopulationFrequencyVariantIndexer.java │ │ │ │ └── VariantIndexer.java │ │ └── executors │ │ │ └── VariantAnnotationCommandExecutor.java │ │ └── validation │ │ ├── TranscriptConsequence.java │ │ └── VEPVariant.java │ └── test │ ├── java │ └── org │ │ └── opencb │ │ ├── cellbase │ │ └── app │ │ │ └── cli │ │ │ ├── VariantAnnotationCommandExecutorTest.java │ │ │ └── main │ │ │ └── annotation │ │ │ └── VcfStringAnnotatorTaskTest.java │ │ └── fetcher │ │ └── GenerateCellbaseLibPropertiesTest.java │ └── resources │ ├── clinvarExample.xml │ ├── cosmicTest.csv │ ├── dbSnpTest.gz │ ├── dbSnpTest.gz.tbi │ ├── disGeNetTest.csv │ ├── gwasTest.csv │ ├── variant │ └── annotation │ │ ├── Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz │ │ ├── Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz.fai │ │ ├── Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz.gzi │ │ ├── commandExecutor │ │ ├── additionalPopulationFrequency │ │ │ ├── Homo_sapiens.1.vcf.gz │ │ │ └── chr1.2017-12-27_01_12.hgva.freq.cellbase.test.json.gz │ │ ├── configuration.json │ │ ├── customAnnotation │ │ │ ├── GEL_GL_6628.duprem.sites.annot.subset.atomic.left.split.test.vcf.gz │ │ │ ├── proband.duprem.atomic.left.split.vcf.gz │ │ │ └── twoCustomFiles │ │ │ │ ├── GEL_GL_6628.duprem.sites.annot.subset.atomic.left.split.test.vcf.gz │ │ │ │ └── GEL_GL_another.duprem.sites.annot.subset.atomic.left.split.test.vcf.gz │ │ └── proteinChangeMatch │ │ │ ├── clinical_variants.full.json.gz │ │ │ ├── gene.json.gz │ │ │ └── proband.duprem.atomic.left.split.vcf.gz │ │ └── sample1_sample2.vcf.gz │ ├── variationParser │ ├── genotype_code.txt.gz │ ├── seq_region.txt.gz │ ├── source.txt.gz │ ├── transcript_variation.txt.gz │ ├── variation.txt.gz │ ├── variation_feature.txt.gz │ └── variation_synonym.txt.gz │ └── vep-example-output.txt ├── cellbase-client ├── pom.xml └── src │ ├── main │ ├── R │ │ ├── .Rbuildignore │ │ ├── .travis.yml │ │ ├── DESCRIPTION │ │ ├── NAMESPACE │ │ ├── NEWS │ │ ├── R │ │ │ ├── AllClasses.R │ │ │ ├── AllGenerics.R │ │ │ ├── CellBaseParam-methods.R │ │ │ ├── CellBaseR-methods.R │ │ │ ├── cbAnnotateVcf-methods.R │ │ │ ├── cbChromosomeInfoClient-methods.R │ │ │ ├── cbClinicalClient-methods.R │ │ │ ├── cbData-methods.R │ │ │ ├── cbGeneClient-methods.R │ │ │ ├── cbGet-methods.R │ │ │ ├── cbProteinClient-methods.R │ │ │ ├── cbRegionClient-methods.R │ │ │ ├── cbSnpClient-methods.R │ │ │ ├── cbSpeciesClient-methods.R │ │ │ ├── cbTfbsClient-methods.R │ │ │ ├── cbTranscriptClient-methods.R │ │ │ ├── cbVariantClient-methods.R │ │ │ ├── cbXrefClient-methods.R │ │ │ ├── cellbase.R │ │ │ ├── commons.R │ │ │ ├── show-methods.R │ │ │ └── tools.R │ │ ├── README.md │ │ ├── man │ │ │ ├── Annovcf.Rd │ │ │ ├── CellBaseParam-class.Rd │ │ │ ├── CellBaseParam.Rd │ │ │ ├── CellBaseR-class.Rd │ │ │ ├── CellBaseR.Rd │ │ │ ├── CellBaseResponse-class.Rd │ │ │ ├── cbAnnotateVcf-CellBaseR-method.Rd │ │ │ ├── cbChromosomeInfoClient-CellBaseR-method.Rd │ │ │ ├── cbClinicalClient-CellBaseR-method.Rd │ │ │ ├── cbData-CellBaseResponse-method.Rd │ │ │ ├── cbGeneClient-CellBaseR-method.Rd │ │ │ ├── cbGet-CellBaseR-method.Rd │ │ │ ├── cbHelp.Rd │ │ │ ├── cbProteinClient-CellBaseR-method.Rd │ │ │ ├── cbRegionClient-CellBaseR-method.Rd │ │ │ ├── cbSnpClient-CellBaseR-method.Rd │ │ │ ├── cbSpeciesClient-CellBaseR-method.Rd │ │ │ ├── cbSpeciesClient.Rd │ │ │ ├── cbTfbsClient-CellBaseR-method.Rd │ │ │ ├── cbTranscriptClient-CellBaseR-method.Rd │ │ │ ├── cbVariantClient-CellBaseR-method.Rd │ │ │ ├── cbXrefClient-CellBaseR-method.Rd │ │ │ ├── cellbaseR-package.Rd │ │ │ ├── createGeneModel.Rd │ │ │ ├── show-CellBaseParam-method.Rd │ │ │ ├── show-CellBaseR-method.Rd │ │ │ └── show-CellBaseResponse-method.Rd │ │ └── vignettes │ │ │ └── cellbaseR.Rmd │ ├── java │ │ └── org │ │ │ └── opencb │ │ │ └── cellbase │ │ │ └── client │ │ │ ├── config │ │ │ ├── ClientConfiguration.java │ │ │ └── RestConfig.java │ │ │ └── rest │ │ │ ├── CellBaseClient.java │ │ │ ├── ClinicalVariantClient.java │ │ │ ├── FeatureClient.java │ │ │ ├── GeneClient.java │ │ │ ├── GenericClient.java │ │ │ ├── GenomicRegionClient.java │ │ │ ├── MetaClient.java │ │ │ ├── ParentRestClient.java │ │ │ ├── ProteinClient.java │ │ │ ├── TranscriptClient.java │ │ │ ├── VariantClient.java │ │ │ ├── VariationClient.java │ │ │ └── models │ │ │ ├── GroupByFields.java │ │ │ ├── GroupCount.java │ │ │ └── mixin │ │ │ └── DrugResponseClassificationMixIn.java │ ├── python │ │ ├── Dockerfile │ │ ├── HISTORY.rst │ │ ├── LICENSE.txt │ │ ├── MANIFEST.in │ │ ├── README.rst │ │ ├── pycellbase │ │ │ ├── __init__.py │ │ │ ├── cbclient.py │ │ │ ├── cbconfig.py │ │ │ ├── cbrestclients.py │ │ │ └── commons.py │ │ ├── python-build.sh │ │ ├── requirements.txt │ │ ├── setup.cfg │ │ ├── setup.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_cbcclient.py │ │ │ ├── test_cbconfig.py │ │ │ ├── test_cbrestclients.py │ │ │ ├── test_commons.py │ │ │ └── testresources │ │ │ │ ├── config.json │ │ │ │ └── config.yml │ │ ├── tools │ │ │ └── cbtools.py │ │ └── use_case.ipynb │ └── resources │ │ └── client-configuration.yml │ └── test │ ├── java │ └── org │ │ └── opencb │ │ └── cellbase │ │ └── client │ │ ├── config │ │ └── ClientConfigurationTest.java │ │ └── rest │ │ ├── CellbaseClientProvider.java │ │ ├── ClinicalVariantClientTest.java │ │ ├── GeneClientTest.java │ │ ├── GenericClientTest.java │ │ ├── GenomicRegionClientTest.java │ │ ├── MetaClientTest.java │ │ ├── ProteinClientTest.java │ │ ├── TranscriptClientTest.java │ │ └── VariantClientTest.java │ └── resources │ └── client-configuration-test.yml ├── cellbase-core ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── opencb │ │ │ └── cellbase │ │ │ └── core │ │ │ ├── ParamConstants.java │ │ │ ├── api │ │ │ ├── ClinicalVariantQuery.java │ │ │ ├── FileQuery.java │ │ │ ├── GeneQuery.java │ │ │ ├── GenomeQuery.java │ │ │ ├── OntologyQuery.java │ │ │ ├── PharmaChemicalQuery.java │ │ │ ├── ProteinQuery.java │ │ │ ├── PublicationQuery.java │ │ │ ├── RegulationQuery.java │ │ │ ├── RepeatsQuery.java │ │ │ ├── SnpQuery.java │ │ │ ├── TfbsQuery.java │ │ │ ├── TranscriptQuery.java │ │ │ ├── VariantQuery.java │ │ │ ├── XrefQuery.java │ │ │ ├── key │ │ │ │ ├── ApiKeyJwtPayload.java │ │ │ │ ├── ApiKeyLicensedDataUtils.java │ │ │ │ ├── ApiKeyManager.java │ │ │ │ ├── ApiKeyQuota.java │ │ │ │ └── ApiKeyStats.java │ │ │ └── query │ │ │ │ ├── AbstractQuery.java │ │ │ │ ├── CellBaseQueryOptions.java │ │ │ │ ├── LogicalList.java │ │ │ │ ├── ProjectionQueryOptions.java │ │ │ │ ├── QueryException.java │ │ │ │ └── QueryParameter.java │ │ │ ├── common │ │ │ ├── GitRepositoryState.java │ │ │ ├── IntervalFeatureFrequency.java │ │ │ ├── Species.java │ │ │ ├── clinical │ │ │ │ ├── ClinicalVariant.java │ │ │ │ ├── ClinicalVariation.java │ │ │ │ ├── ClinvarPublicSet.java │ │ │ │ ├── Cosmic.java │ │ │ │ └── gwas │ │ │ │ │ ├── Gwas.java │ │ │ │ │ ├── GwasStudy.java │ │ │ │ │ ├── GwasTest.java │ │ │ │ │ └── GwasTrait.java │ │ │ ├── drug │ │ │ │ ├── Drug.java │ │ │ │ ├── DrugPartnerInteraction.java │ │ │ │ ├── Interactor.java │ │ │ │ ├── Partner.java │ │ │ │ └── XRef.java │ │ │ └── regulatory │ │ │ │ ├── Pwm.java │ │ │ │ ├── RegulatoryRegion.java │ │ │ │ └── Tfbs.java │ │ │ ├── config │ │ │ ├── CellBaseConfiguration.java │ │ │ ├── DatabaseCredentials.java │ │ │ ├── Databases.java │ │ │ ├── DownloadProperties.java │ │ │ ├── MongoDBDatabaseCredentials.java │ │ │ ├── Rest.java │ │ │ ├── ServerProperties.java │ │ │ ├── SpeciesConfiguration.java │ │ │ └── SpeciesProperties.java │ │ │ ├── exception │ │ │ └── CellBaseException.java │ │ │ ├── models │ │ │ ├── DataRelease.java │ │ │ └── DataReleaseSource.java │ │ │ ├── result │ │ │ ├── CellBaseDataResponse.java │ │ │ └── CellBaseDataResult.java │ │ │ ├── serializer │ │ │ ├── CellBaseFileSerializer.java │ │ │ ├── CellBaseJsonFileSerializer.java │ │ │ └── CellBaseSerializer.java │ │ │ ├── utils │ │ │ ├── BioUtils.java │ │ │ └── SpeciesUtils.java │ │ │ └── variant │ │ │ ├── AnnotationBasedPhasedQueryManager.java │ │ │ ├── ClinicalPhasedQueryManager.java │ │ │ ├── CustomAnnotationPhasedQueryManager.java │ │ │ ├── PhasedQueryManager.java │ │ │ └── PopulationFrequencyPhasedQueryManager.java │ └── resources │ │ ├── configuration.yml │ │ ├── log4j2.console.xml │ │ ├── log4j2.file.xml │ │ ├── log4j2.xml │ │ └── org │ │ └── opencb │ │ └── cellbase │ │ └── core │ │ └── variation │ │ └── variation_consequences.properties │ └── test │ ├── java │ └── org │ │ └── opencb │ │ └── cellbase │ │ └── core │ │ ├── GeneQueryTest.java │ │ ├── OntologyQueryTest.java │ │ ├── TranscriptQueryTest.java │ │ ├── config │ │ └── CellBaseConfigurationTest.java │ │ └── variant │ │ └── VariantAnnotatorRunnerTest.java │ └── resources │ ├── configuration.yml │ ├── gene.json │ └── hgvs │ └── gene.test.json.gz ├── cellbase-lib ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── opencb │ │ │ └── cellbase │ │ │ └── lib │ │ │ ├── EtlCommons.java │ │ │ ├── MongoDBCollectionConfiguration.java │ │ │ ├── builders │ │ │ ├── CaddAllAnnotationBuilder.java │ │ │ ├── CaddScoreBuilder.java │ │ │ ├── CellBaseBuilder.java │ │ │ ├── ConservationBuilder.java │ │ │ ├── DbSnpBuilder.java │ │ │ ├── DrugParser.java │ │ │ ├── EnsemblGeneBuilderIndexer.java │ │ │ ├── GeneBuilder.java │ │ │ ├── GeneBuilderIndexer.java │ │ │ ├── GeneBuilderUtils.java │ │ │ ├── GeneExpressionAtlasBuilder.java │ │ │ ├── GenomeSequenceFastaBuilder.java │ │ │ ├── InteractionBuilder.java │ │ │ ├── OntologyBuilder.java │ │ │ ├── PharmGKBBuilder.java │ │ │ ├── ProteinBuilder.java │ │ │ ├── PubMedBuilder.java │ │ │ ├── RefSeqGeneBuilder.java │ │ │ ├── RefSeqGeneBuilderIndexer.java │ │ │ ├── RegulatoryFeatureBuilder.java │ │ │ ├── RegulatoryRegionBuilder.java │ │ │ ├── RepeatsBuilder.java │ │ │ ├── RevelScoreBuilder.java │ │ │ ├── RocksDbManager.java │ │ │ ├── SpliceBuilder.java │ │ │ ├── VariationBuilder.java │ │ │ ├── clinical │ │ │ │ └── variant │ │ │ │ │ ├── ClinVarIndexer.java │ │ │ │ │ ├── ClinVarParser.java │ │ │ │ │ ├── ClinicalIndexer.java │ │ │ │ │ ├── ClinicalVariantBuilder.java │ │ │ │ │ ├── CosmicBuilder.java │ │ │ │ │ ├── CosmicIndexer.java │ │ │ │ │ ├── CosmicIndexerCallback.java │ │ │ │ │ ├── DOCMIndexer.java │ │ │ │ │ ├── GwasIndexer.java │ │ │ │ │ ├── HGMDIndexer.java │ │ │ │ │ └── IARCTP53Indexer.java │ │ │ ├── formats │ │ │ │ ├── Cadd.java │ │ │ │ ├── ConservedRegionFeature.java │ │ │ │ ├── GeneExpressionAtlas.java │ │ │ │ └── Genome.java │ │ │ └── utils │ │ │ │ └── GenomeSequenceUtils.java │ │ │ ├── db │ │ │ └── MongoDBManager.java │ │ │ ├── download │ │ │ ├── AbstractDownloadManager.java │ │ │ ├── CaddDownloadManager.java │ │ │ ├── ClinicalDownloadManager.java │ │ │ ├── CoreDownloadManager.java │ │ │ ├── DownloadFile.java │ │ │ ├── DownloadManager.java │ │ │ ├── Downloader.java │ │ │ ├── GeneDownloadManager.java │ │ │ ├── GenomeDownloadManager.java │ │ │ ├── MissenseScoresDownloadManager.java │ │ │ ├── OntologyDownloadManager.java │ │ │ ├── PharmGKBDownloadManager.java │ │ │ ├── ProteinDownloadManager.java │ │ │ ├── PubMedDownloadManager.java │ │ │ ├── RegulationDownloadManager.java │ │ │ └── VariationDownloadManager.java │ │ │ ├── impl │ │ │ └── core │ │ │ │ ├── CellBaseCoreDBAdaptor.java │ │ │ │ ├── CellBaseDBAdaptor.java │ │ │ │ ├── ClinicalMongoDBAdaptor.java │ │ │ │ ├── GeneMongoDBAdaptor.java │ │ │ │ ├── GenomeMongoDBAdaptor.java │ │ │ │ ├── MetaMongoDBAdaptor.java │ │ │ │ ├── MissenseVariationFunctionalScoreMongoDBAdaptor.java │ │ │ │ ├── MongoDBAdaptor.java │ │ │ │ ├── MongoDBAdaptorFactory.java │ │ │ │ ├── OntologyMongoDBAdaptor.java │ │ │ │ ├── PharmacogenomicsMongoDBAdaptor.java │ │ │ │ ├── ProteinMongoDBAdaptor.java │ │ │ │ ├── PublicationMongoDBAdaptor.java │ │ │ │ ├── RegulationMongoDBAdaptor.java │ │ │ │ ├── ReleaseMongoDBAdaptor.java │ │ │ │ ├── RepeatsMongoDBAdaptor.java │ │ │ │ ├── SnpMongoDBAdaptor.java │ │ │ │ ├── SpliceScoreMongoDBAdaptor.java │ │ │ │ ├── TranscriptMongoDBAdaptor.java │ │ │ │ ├── VariantMongoDBAdaptor.java │ │ │ │ ├── XRefMongoDBAdaptor.java │ │ │ │ └── converters │ │ │ │ └── VariantConverter.java │ │ │ ├── indexer │ │ │ └── IndexManager.java │ │ │ ├── install │ │ │ ├── InstallManager.java │ │ │ └── MongoDBShardUtils.java │ │ │ ├── iterator │ │ │ ├── ApiKeyFilteredVariantIterator.java │ │ │ ├── CellBaseIterator.java │ │ │ ├── CellBaseMongoDBIterator.java │ │ │ └── VariantMongoDBIterator.java │ │ │ ├── loader │ │ │ ├── CellBaseLoader.java │ │ │ ├── CellBaseTypeConverter.java │ │ │ ├── LoadRunner.java │ │ │ ├── LoaderException.java │ │ │ └── MongoDBCellBaseLoader.java │ │ │ ├── managers │ │ │ ├── AbstractManager.java │ │ │ ├── AggregationApi.java │ │ │ ├── CellBaseManagerFactory.java │ │ │ ├── ClinicalManager.java │ │ │ ├── DataReleaseManager.java │ │ │ ├── FeatureApi.java │ │ │ ├── FileManager.java │ │ │ ├── GeneManager.java │ │ │ ├── GenomeManager.java │ │ │ ├── MetaManager.java │ │ │ ├── OntologyManager.java │ │ │ ├── PharmacogenomicsManager.java │ │ │ ├── ProteinManager.java │ │ │ ├── PublicationManager.java │ │ │ ├── RegulatoryManager.java │ │ │ ├── RepeatsManager.java │ │ │ ├── TfbsManager.java │ │ │ ├── TranscriptManager.java │ │ │ ├── VariantManager.java │ │ │ └── XrefManager.java │ │ │ ├── monitor │ │ │ └── Monitor.java │ │ │ └── variant │ │ │ ├── VariantAnnotationUtils.java │ │ │ ├── annotation │ │ │ ├── CellBaseNormalizerSequenceAdaptor.java │ │ │ ├── ConsequenceTypeBNDCalculator.java │ │ │ ├── ConsequenceTypeCNVGainCalculator.java │ │ │ ├── ConsequenceTypeCalculator.java │ │ │ ├── ConsequenceTypeDeletionCalculator.java │ │ │ ├── ConsequenceTypeGenericRegionCalculator.java │ │ │ ├── ConsequenceTypeInsertionCalculator.java │ │ │ ├── ConsequenceTypeMNVCalculator.java │ │ │ ├── ConsequenceTypeSNVCalculator.java │ │ │ ├── UnsupportedURLVariantFormat.java │ │ │ ├── VariantAnnotationCalculator.java │ │ │ ├── VariantAnnotator.java │ │ │ └── futures │ │ │ │ ├── FuturePharmacogenomicsAnnotator.java │ │ │ │ ├── FutureSnpAnnotator.java │ │ │ │ └── FutureSpliceScoreAnnotator.java │ │ │ └── hgvs │ │ │ ├── BuildingComponents.java │ │ │ ├── CdnaCoord.java │ │ │ ├── HgvsCalculator.java │ │ │ ├── HgvsProtein.java │ │ │ ├── HgvsProteinCalculator.java │ │ │ ├── HgvsTranscriptCalculator.java │ │ │ └── TranscriptUtils.java │ └── resources │ │ └── mongodb-indexes.json │ └── test │ ├── java │ └── org │ │ └── opencb │ │ └── cellbase │ │ └── lib │ │ ├── GenericMongoDBAdaptorTest.java │ │ ├── SpeciesUtilsTest.java │ │ ├── builders │ │ ├── CaddScoreParserTest.java │ │ ├── ConservationBuilderTest.java │ │ ├── GeneBuilderTest.java │ │ ├── GenericBuilderTest.java │ │ ├── PharmGKBBuilderTest.java │ │ ├── RefSeqGeneBuilderTest.java │ │ ├── RegulatoryFeatureBuilderTest.java │ │ ├── RepeatsBuilderTest.java │ │ ├── RevelScoreBuilderTest.java │ │ ├── SpliceBuilderTest.java │ │ ├── clinical │ │ │ └── variant │ │ │ │ └── ClinicalVariantBuilderTest.java │ │ └── utils │ │ │ └── GenomeSequenceUtilsTest.java │ │ ├── impl │ │ └── core │ │ │ ├── CellBaseNormalizerSequenceAdaptorTest.java │ │ │ ├── ClinicalMongoDBAdaptorTest.java │ │ │ ├── GeneMongoDBAdaptorTest.java │ │ │ ├── GenomeMongoDBAdaptorTest.java │ │ │ ├── MongoDBAdaptorFactoryTest.java │ │ │ ├── PharmacogenomicsMongoDBAdaptorTest.java │ │ │ ├── ProteinMongoDBAdaptorTest.java │ │ │ ├── TranscriptMongoDBAdaptorTest.java │ │ │ ├── VariantAnnotationCalculatorTest.java │ │ │ ├── VariantMongoDBAdaptorTest.java │ │ │ └── XRefMongoDBAdaptorTest.java │ │ ├── indexer │ │ └── IndexManagerTest.java │ │ ├── managers │ │ ├── ApiKeyManagerTest.java │ │ └── DataReleaseManagerTest.java │ │ ├── monitor │ │ └── MonitorTest.java │ │ └── variant │ │ ├── ClinicalManagerTest.java │ │ ├── VariantManagerTest.java │ │ └── hgvs │ │ ├── HgvsCalculatorTest.java │ │ ├── HgvsProteinCalculatorTest.java │ │ └── HgvsTranscriptCalculatorTest.java │ └── resources │ ├── caddTest.tsv.gz │ ├── caddTest.tsv.gz.tbi │ ├── cadd_example.txt.gz │ ├── clinicalMongoDBAdaptor │ ├── gene_list.json.gz │ ├── nativeGet │ │ └── clinical_variants.full.test.json.gz │ └── phasedQueries │ │ └── clinical_variants.full.test.json.gz │ ├── clinvar.json.gz │ ├── configuration.test.yaml │ ├── conservation │ ├── gerp │ │ ├── conservation_1.json.gz │ │ ├── conservation_19.json.gz │ │ ├── conservation_2.json.gz │ │ └── gerp.bedGraph.gz │ ├── phastCons │ │ └── empty.wigFix.gz │ └── phylop │ │ └── empty.wigFix.gz │ ├── cosmic.json.gz │ ├── dgv.json.gz │ ├── dgv.txt.gz │ ├── gene.test.json.gz │ ├── gene │ ├── ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt │ ├── Homo_sapiens.GRCh38.fa │ ├── Homo_sapiens.GRCh38.fa.fai │ ├── all_gene_disease_associations.tsv.gz │ ├── allgenes_updown_in_organism_part.tab.gz │ ├── description.txt │ ├── dgidb.tsv │ ├── gene-test.json.gz │ ├── gnomad.v2.1.1.lof_metrics.by_transcript.txt.gz │ ├── goa_human.gaf.gz │ ├── homo_sapiens.cdna.all.fa.gz │ ├── homo_sapiens.gtf.gz │ ├── homo_sapiens.pep.all.fa.gz │ ├── phenotype_to_genes.txt │ └── xrefs.txt │ ├── gene_refseq │ ├── refSeq_Homo_sapiens.GRCh38_protein.faa.gz │ ├── refseq_test_cdna.fna.gz │ └── unittest.gtf │ ├── genome │ ├── genome_info.json │ └── genome_sequence.test.json.gz │ ├── gnomad.v2.1.1.lof_metrics.by_transcript.txt.gz │ ├── gwas.json.gz │ ├── hgvs │ ├── gene.test.json.gz │ ├── gene_grch38.test.json.gz │ ├── genome_sequence.test.json.gz │ └── genome_sequence_grch38.test.json.gz │ ├── idmapping_selected.tab.gz │ ├── index │ └── mongodb-indexes.json │ ├── ontology │ ├── go-basic.obo │ └── goa_human.gaf │ ├── protein │ └── protein.test.json.gz │ ├── regulation │ ├── Regulatory_Build.regulatory_features.gff.gz │ ├── hsa_MTI.xlsx │ ├── miRNA.xls │ ├── motif_features.gff.gz │ └── motif_features.gff.gz.tbi │ ├── repeats │ ├── genomicSuperDups.txt.gz │ ├── repeats.test.json.gz │ ├── simpleRepeat.txt.gz │ └── windowMasker.txt.gz │ ├── revel │ ├── missense_variation_functional_score.json.gz │ ├── revel_grch38_all_chromosomes.csv │ └── revel_grch38_all_chromosomes.csv.zip │ ├── splice │ └── mmsplice │ │ ├── mmspliceScores.csv.gz │ │ └── mmspliceVersion.json │ ├── transcript │ └── gene.test.json.gz │ ├── variant-annotation-test.json.gz │ ├── variant-annotation │ ├── clinical_variants.cosmic.test.json.gz │ ├── clinical_variants.test.json.gz │ ├── clinvar_chunks │ │ └── clinical_variants.test.json.gz │ ├── gene.test.json.gz │ ├── genome_sequence.test.json.gz │ ├── prot_func_pred_chr_13.test.json.gz │ ├── prot_func_pred_chr_18.test.json.gz │ ├── prot_func_pred_chr_19.test.json.gz │ ├── prot_func_pred_chr_MT.test.json.gz │ ├── protein.test.json.gz │ ├── regulatory_region.test.json.gz │ ├── repeats.json.gz │ ├── structuralVariants.json.gz │ ├── variation_chr1.full.test.json.gz │ ├── variation_chr19.full.test.json.gz │ ├── variation_chr2.full.test.json.gz │ └── variation_chrMT.full.test.json.gz │ ├── variant │ └── annotation │ │ ├── Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz │ │ ├── Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz.fai │ │ ├── Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz.gzi │ │ ├── clinicalVariant │ │ ├── ClinVarFullRelease_2020-02.xml.gz │ │ ├── CosmicMutantExport.tsv.gz │ │ ├── datasets │ │ │ ├── germlineMutationDataIARC TP53 Database, R20.txt │ │ │ ├── germlineMutationReferenceIARC TP53 Database, R20.txt │ │ │ ├── somaticMutationDataIARC TP53 Database, R20.txt │ │ │ └── somaticMutationReferenceIARC TP53 Database, R20.txt │ │ ├── docm.json.gz │ │ ├── variant_summary.txt.gz │ │ └── variation_allele.txt.gz │ │ └── sample1_sample2.vcf.gz │ ├── variation_chr1.full.test.json.gz │ ├── variation_chr10.full.test.json.gz │ ├── variation_chr17.full.test.json.gz │ ├── variation_chr22.full.test.json.gz │ ├── wigVarStepExampleSmallChr21.bw │ └── xref │ └── gene.test.json.gz ├── cellbase-server ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── opencb │ │ └── cellbase │ │ └── server │ │ ├── RestServer.java │ │ ├── exception │ │ ├── CellBaseServerException.java │ │ ├── LimitException.java │ │ ├── SpeciesException.java │ │ └── VersionException.java │ │ └── rest │ │ ├── AdminRestWebService.java │ │ ├── CORSFilter.java │ │ ├── CellBaseExceptionMapper.java │ │ ├── FileWSServer.java │ │ ├── GenericRestWSServer.java │ │ ├── IWSServer.java │ │ ├── MetaWSServer.java │ │ ├── OntologyWSServer.java │ │ ├── PublicationWSServer.java │ │ ├── SpeciesWSServer.java │ │ ├── clinical │ │ ├── ClinicalWSServer.java │ │ └── PharmacogenomicsWSServer.java │ │ ├── feature │ │ ├── GeneWSServer.java │ │ ├── IdWSServer.java │ │ ├── ProteinWSServer.java │ │ └── TranscriptWSServer.java │ │ ├── genomic │ │ ├── ChromosomeWSServer.java │ │ ├── RegionWSServer.java │ │ └── VariantWSServer.java │ │ ├── network │ │ ├── DotServer.java │ │ ├── PathwayWSServer.java │ │ ├── PathwayWSServerMongo.java │ │ └── ProteinProteinInteractionWSServer.java │ │ ├── regulatory │ │ ├── RegulatoryWSServer.java │ │ └── TfWSServer.java │ │ └── utils │ │ └── UtilsWSServer.java │ └── webapp │ ├── META-INF │ └── MANIFEST.MF │ ├── WEB-INF │ └── web.xml │ ├── index.old.html │ └── webservices │ ├── index.html │ └── swagger-ui │ ├── css │ ├── print.css │ ├── reset.css │ ├── screen.css │ ├── style.css │ └── typography.css │ ├── fonts │ ├── droid-sans-v6-latin-700.eot │ ├── droid-sans-v6-latin-700.svg │ ├── droid-sans-v6-latin-700.ttf │ ├── droid-sans-v6-latin-700.woff │ ├── droid-sans-v6-latin-700.woff2 │ ├── droid-sans-v6-latin-regular.eot │ ├── droid-sans-v6-latin-regular.svg │ ├── droid-sans-v6-latin-regular.ttf │ ├── droid-sans-v6-latin-regular.woff │ └── droid-sans-v6-latin-regular.woff2 │ ├── images │ ├── explorer_icons.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ ├── favicon.ico │ ├── logo_small.png │ ├── pet_store_api.png │ ├── throbber.gif │ └── wordnik_api.png │ ├── lang │ ├── en.js │ ├── es.js │ ├── pt.js │ ├── ru.js │ └── translator.js │ ├── lib │ ├── backbone-min.js │ ├── handlebars-2.0.0.js │ ├── highlight.7.3.pack.js │ ├── jquery-1.8.0.min.js │ ├── jquery.ba-bbq.min.js │ ├── jquery.slideto.min.js │ ├── jquery.wiggle.min.js │ ├── marked.js │ ├── swagger-oauth.js │ ├── underscore-min.js │ └── underscore-min.map │ ├── o2c.html │ ├── swagger-ui.js │ └── swagger-ui.min.js ├── cellbase-test ├── README.md ├── fitnesse │ └── FitNesseRoot │ │ ├── CellBase │ │ ├── CellBaseCompleteSuite.wiki │ │ ├── CellBaseCompleteSuite │ │ │ ├── GeneralTests.wiki │ │ │ ├── GeneralTests │ │ │ │ └── MetaTests.wiki │ │ │ ├── HSapiensTests.wiki │ │ │ ├── HSapiensTests │ │ │ │ ├── ClinicalTests.wiki │ │ │ │ ├── GeneTests.wiki │ │ │ │ ├── GenomeSequenceTests.wiki │ │ │ │ ├── ProteinTests.wiki │ │ │ │ ├── RegionTests.wiki │ │ │ │ ├── RegulationTests.wiki │ │ │ │ ├── SpeciesTests.wiki │ │ │ │ ├── TFBSTests.wiki │ │ │ │ ├── TranscriptTests.wiki │ │ │ │ ├── VariantTests.wiki │ │ │ │ ├── VariationTests.wiki │ │ │ │ └── XrefTests.wiki │ │ │ └── SuiteSetUp.wiki │ │ ├── content.txt │ │ └── properties.xml │ │ ├── FrontPage │ │ ├── content.txt │ │ └── properties.xml │ │ ├── PageFooter │ │ ├── content.txt │ │ └── properties.xml │ │ ├── PageHeader │ │ ├── content.txt │ │ └── properties.xml │ │ ├── RecentChanges.wiki │ │ ├── TemplateLibrary │ │ ├── StaticPage │ │ │ ├── content.txt │ │ │ └── properties.xml │ │ 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