This module implements alignment data output in various formats.

The interface consists of a single method call that takes GPU buffers post-alignment and accumulates the results in host memory until we have enough data to write out a batch to disk. Additional method calls are used to signal the start/end of a batch of alignment data, as well as to configure the output. The main interface for this module is the OutputFile class, which exposes most of the functionality.

The following classes are exposed as the interface to this module: