Add germline input#3

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Bolladeen wants to merge 5 commits intomasterfrom

add_germline_input

Commits on Nov 7, 2022

mod(scarlet): converted codebase python2 -> python3, removed hardcoded betabinomial pmf
Bolladeen
committed

Commits on Dec 8, 2022

added germline mutation input functionality
Bolladeen
committed

Commits on Dec 13, 2022

changed optimizer time limit to 4 hours
Bolladeen
committed

Commits on Feb 21, 2023