Speed regression

[ktmeaton]

Somewhere between 4756dcee and 967674e9, I made changes that had significant speed impacts :( The sars-cov-2 dataset went down from 100 sequences/sec to < 1 seq/sec 😢 going to walk back those changes to identify the problem.

[ktmeaton]

The culprit is b0961738, let this be a lesson to myself to not make such big changes at a time.

https://github.com/phac-nml/rebar/compare/c644c9730009..b0961738

b0961738 changes:

• Wildcarding in designated parents.
• More thorough compare_parents validation for parent-child relationships.
• Removing min_conflict option for best hypothesis.
• KnockoutRecombinant Hypothesis

[ktmeaton]

It's purely the new KnockoutRecombinant hypothesis! Well that is very curious, but luckily the easiest to undo and troubleshoot.

Update: Maybe not, to be continued!