Genotype Storage

To store and query genomic variants, we use genotype storage.

There are two interfaces that define genotype storage:

When you want to create new genotype storage, you have to create two classes - a genotype storage class that inherits the dae.genotype_storage.genotype_storage.GenotypeStorage and an import storage class that inherits dae.import_tools.import_tools.ImportStorage. Once created, you should register these classes in the two extension points defined in the setup.py:

  • for genotype storage class use [dae.genotype_storage.factories] extenstion point;

  • for import storage class use [dae.import_tools.storages] extenstion point.

As an example of genotype storage definitions, you can check the following pairs of classes:

  • Filesystem storage (filesystem storage type):

    • genotype storage dae.filesystem_storage.in_memory.filesystem_genotype_storage.FilesystemGenotypeStorage

    • import storage: dae.filesystem_storage.in_memory.filesystem_import_storage.FilesystemImportStorage

  • Impala schema 1 storage (impala storage type):

    • genotype storage dae.impala_storage.schema1.impala_genotype_storage.ImpalaGenotypeStorage

    • import storage: dae.impala_storage.schema1.impala_schema1.ImpalaSchema1ImportStorage

  • Impala schema 2 storage (impala2 storage type):

    • genotype storage dae.impala_storage.schema2.schema2_genotype_storage.Schema2GenotypeStorage

    • import storage: dae.impala_storage.schema1.schema2_import_storage.Schema2ImportStorage