refactor: supply boolean args to `pixy`

[emmcauley]

Summary

This PR sets --bypass_invariant_check and --include_multiallelic_snps to more conventional boolean arguments.

Changed

• pixy now accepts more conventional boolean CLI arguments instead of a "yes/no" option.
• Tests have been updated accordingly.
• This is a breaking change: any scripts that try to use the current paradigm (--bypass_invariant_check yes instead of just --bypass_invariant_check) will no longer work.