20x alignment fixes and tests

[benjijamorris]

Pull request recommendations:

• [x ] Name your pull request your-development-type/short-description. Ex: feature/read-tiff-files
• [ x] Link to any relevant issue in the PR description. Ex: Resolves [Issue/size param automation #12], adds tiff file format support
• [ x] Provide context of changes.
• [x ] Provide relevant tests for your feature or bug fix.
• [ x] Provide or update documentation for any feature added by your pull request.

Thanks for contributing!

This fixes a bug in 20x alignment that results in generation of all-nan alignment matrices regardless of input.

[GabeMedrash]

LGTM!