linkageio / hapdab Goto Github PK

Add instructions to the README to install the package

As a researcher, I want a software environment that is modular and backed by other software libraries that are reliable.

Add an optional feature for Cassandra to the minus80 API.

As a programmer, I want a robust and high quality API

I need to know if the philosophy behind the Cassandra schema differs from the one we used for SQLite. I know that Cassandra believes in denormalization so we might be sacrificing efficiency for space (which might have sped up SQLite in the first place)

I think there are beagle test files that do this.

As a developer I need to know the basics on Cassandra and Spark. I need this information to implement the features we are proposing to use.

This test VCF needs to be small enough to fit into the GitHub Repo but large enough to be useful.

As a researcher, I want software that is easy to use, robust, and trusted.

As a researcher, I want to know the accuracy of imputation using the SNP Chip

Value Statement

As a geneticist, I need easy and fast access to genotype data. I need this because I want to be able to quickly explore my data and evaluate genomic structure in regions that interest me. The tools that are out there are hard to use and often require me to stitch many different tools together in order to get the data I want.

Completed When

All tasks assigned to this epic are QA'd and Closed. In general, code pushed to GitHub will be backed by Spark/Cassandra and will cover the use cases we performed in the MNEc2M paper. There will also be benchmarks to identify if this tech is better than the default Minus80 stack.