Pinchas mode

This release includes an option for bacteria only mode (set by adding an environment variable called "BACTERIAONLY" and setting it to TRUE, 1, or any other value that won't evaluate to false.

Modularity improvement

Changes under the hood for faster application to new standards. Functionality and performance appear to be (and should be) unchanged.

Single end and long read logic

Working for single end reads and long reads. Also now using tolerances stored in the reference data for a standard.

First working version

Generates reports as expected and is documented. Can be used in the wild.