GPF Development

• dae Interface
  • Genomic Resources
    • Classes and Functions
      • dae.genomic_resources package
  • Annotation
    • Classes and Functions
      • dae.annotation package
  • Effect Annotation
    • Classes and Functions
      • dae.effect_annotation package
  • Genomic Variants
    • Apache Parquet variants schema
      • Summary Variants/Alleles flat schema
      • Family Variants schema
      • Family Alleles schema
      • Variant Scores schema
      • Pedigree file schema
    • Family variants query interface
      • Query by regions
      • Query by genes and effect types
      • Query by inheritance
      • Query by family IDs
      • Query by person IDs
      • Query by sexes
      • Query by roles
      • Query by variant types
      • Query with real value variant attributes (scores)
      • Query with filter function
    • Genomic Variants Classes and Functions
      • dae.variants package
  • Pedigrees Tools
    • Classes and Functions
      • dae.pedigrees package
  • Variants Loaders
    • dae.variants_loaders package
      • Subpackages
      • Module contents
    • dae.variants_loaders.raw package
      • Submodules
      • dae.variants_loaders.raw.flexible_variant_loader module
      • dae.variants_loaders.raw.loader module
      • Module contents
    • dae.variants_loaders.dae package
      • Submodules
      • dae.variants_loaders.dae.loader module
      • Module contents
    • dae.variants_loaders.vcf package
      • Submodules
      • dae.variants_loaders.vcf.loader module
      • Module contents
    • dae.variants_loaders.cnv package
      • Submodules
      • dae.variants_loaders.cnv.flexible_cnv_loader module
      • dae.variants_loaders.cnv.loader module
      • Module contents
  • Import Tools
    • What is Import Tools
    • Import Tools config files
    • Import Tools configuration format
    • Classes and Functions
      • dae.import_tools package
  • Genotype Data Parquet Writers
    • dae.parquet package
      • Subpackages
      • Module contents
    • dae.parquet.schema1 package
      • Submodules
      • dae.parquet.schema1.parquet_io module
      • dae.parquet.schema1.serializers module
      • Module contents
    • dae.parquet.schema2 package
      • Submodules
      • dae.parquet.schema2.parquet_io module
      • dae.parquet.schema2.serializers module
      • Module contents
  • Query Genomic Variants
    • dae.query_variants package
      • Subpackages
      • Submodules
      • dae.query_variants.attributes_query module
      • dae.query_variants.attributes_query_inheritance module
      • dae.query_variants.query_runners module
      • Module contents
    • dae.query_variants.sql package
      • Subpackages
      • Module contents
    • dae.query_variants.sql.schema1 package
      • Submodules
      • dae.query_variants.sql.schema1.base_query_builder module
      • dae.query_variants.sql.schema1.family_variants_query_builder module
      • dae.query_variants.sql.schema1.schema1_query_director module
      • dae.query_variants.sql.schema1.summary_variants_query_builder module
      • Module contents
    • dae.query_variants.sql.schema2 package
      • Subpackages
      • Submodules
      • dae.query_variants.sql.schema2.base_query_builder module
      • dae.query_variants.sql.schema2.family_builder module
      • dae.query_variants.sql.schema2.summary_builder module
      • Module contents
  • Genotype Storage
    • dae.genotype_storage package
      • Submodules
      • dae.genotype_storage.genotype_storage module
      • dae.genotype_storage.genotype_storage_registry module
      • Module contents
  • In-Memory Genotype Storage
    • dae.inmemory_storage package
      • Submodules
      • dae.inmemory_storage.inmemory_genotype_storage module
      • dae.inmemory_storage.inmemory_import_storage module
      • dae.inmemory_storage.raw_variants module
      • Module contents
  • Impala Genotype Storages
    • dae.impala_storage package
      • Subpackages
      • Module contents
    • dae.impala_storage.helpers package
      • Submodules
      • dae.impala_storage.helpers.hdfs_helpers module
      • dae.impala_storage.helpers.impala_helpers module
      • dae.impala_storage.helpers.rsync_helpers module
      • Module contents
    • dae.impala_storage.schema1 package
      • Submodules
      • dae.impala_storage.schema1.impala_genotype_storage module
      • dae.impala_storage.schema1.impala_schema1 module
      • dae.impala_storage.schema1.impala_variants module
      • dae.impala_storage.schema1.import_commons module
      • Module contents
    • dae.impala_storage.schema2 package
      • Submodules
      • dae.impala_storage.schema2.bigquery_variants module
      • dae.impala_storage.schema2.impala_variants module
      • dae.impala_storage.schema2.schema2_genotype_storage module
      • dae.impala_storage.schema2.schema2_import_storage module
      • dae.impala_storage.schema2.sql_query_runner module
      • Module contents
  • Configuration
    • Classes and Functions
      • dae.configuration package
  • Genotype Data
    • Classes and Functions
      • dae.studies package
  • Phenotype Data
    • Pheno DB access
    • Example usage of PhenoDB
    • Classes and Functions
      • dae.pheno package
  • Phenotype tool
    • Example usage of PhenoTool class
    • Example usage of PhenoTool class with pheno filters
    • Example with vineland_ii
    • Classes and Functions
      • dae.pheno_tool package
  • Enrichment Tool
    • Example usage of EnrichmentTool class
    • Classes and Functions
      • dae.pheno_tool package
  • Gene Properties
    • Example usage of Weights class
    • Classes and Functions
      • dae.gene package
  • Tools
    • Classes and Functions
      • dae.annotation package
• wdae Interface
  • Genotype browser
  • genotype_browser package
    • Module contents
      • GenotypeBrowserQueryView
  • users_api package
    • Module contents
      • AuthenticationLog
      • BaseVerificationCode
      • ResetPasswordCode
      • SetPasswordCode
      • WdaeUser
      • WdaeUserManager
      • group_post_delete()
      • group_pre_delete()
      • staff_update()
      • BasePasswordView
      • ForgotPassword
      • ResetPassword
      • SetPassword
      • UserViewSet
      • WdaeLoginView
      • change_password()
      • check_verif_code()
      • get_federation_credentials()
      • get_user_info()
      • iterator_to_json()
      • logout()
      • register()
      • revoke_federation_credentials()
      • SessionAuthenticationWithUnauthenticatedCSRF
      • SessionAuthenticationWithoutCSRF
      • CreatableSlugRelatedField
      • DatasetSerializer
      • UserSerializer
      • UserWithoutEmailSerializer
      • SomeSuperuserLeftValidator