APIs

Overview

In addition to the native C++ interface, GenomicsDB has support/bindings for Python, Java, and R. The data structure returned from a GenomicsDB query depends on the API or CLI tool being used and the method invoked. Similarly, the method of passing in query field information depends on the route chosen.

The various APIs take in the same query fields in one form or another, so check the appropriate reference for your use case. If you are new to GenomicsDB, we recommend starting with the gt_mpi_gather CLI tool to familiarize yourself with the concepts.

All the APIs support taking configuration options as protobuf. Here’s the protobuf documentation:

GenomicsDB Protobuf Documentation

C++

Native interface - See cpp source code
Querying CLI tools available - see vcf2genomicsdb

API Reference

C++ Query Interface

Python

Python bindings for GenomicsDB. Requires Python version >= 3.6
Built using Cython.
Currently only supports querying (no importing).
Data can be returned in either a numpy matrix or a list of lists.

The GenomicsDB python bindings are published on PyPI (currently experimental).

Install genomicsdb with the following command:

pip install genomicsdb

API Reference

genomicsdb module

Java

Data can be returned in either a htsjdk VariantContext object or <other>.
The GenomicsDB java bindings are published to Maven Central every release.
Add GenomicsDB to your maven project with the following snippet (update the version, if necessary):

<!-- https://mvnrepository.com/artifact/org.genomicsdb/genomicsdb -->
<dependency>
   <groupId>org.genomicsdb</groupId>
   <artifactId>genomicsdb</artifactId>
   <version>1.4.5</version>
</dependency>