Remove reliance on MD tags

[fnothaft]

MD tags are arcane and poorly spec'd. Even further, many aligners don't emit MD tags. We're currently relying on MD tags for BQSR, INDEL realignment, etc. We should eliminate them from the codebase (and eliminate their "promotion" into the schema upstream?) to both eliminate complexity and to improve robustness.

I've eliminated the use of MD tags downstream in avocado.

[fnothaft]

This issue only BQSR and INDEL realignment. #1412 resolves this for INDEL realignment, and #1358 will resolve this for BQSR. Closing this in favor of those more targeted tickets/PRs.