Port PMD error model from BEAST1 - Githubissues

bioDS / beast-phylonco

A BEAST2 package for single-cell cancer evolution

GNU Lesser General Public License v2.1

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Port PMD error model from BEAST1 #22

Open kche309 opened 2 years ago

kche309 commented 2 years ago

Port DNA damage model from BEAST1

See related Git Issue from the Beast2 repo https://github.com/CompEvol/beast2/issues/173

Preliminary version to be implemented in April.

kche309 commented 2 years ago

Work in progress on branch https://github.com/bioDS/beast-phylonco/tree/PMDErrorModel

TODOs:

~refactor ErrorModel superclass to take branching time t~
~In Likelihood class, pass branch time into error models methods~
Unit testing
Example XML template for PMD error model

kche309 commented 2 years ago

Refactored error model class to take in branch time t https://github.com/bioDS/beast-phylonco/commit/9c058c40ec61966b4ac5d51e27d83a3db20a0240 Added a taxa exclusion list, which means the excluded taxa are assumed to be error-free https://github.com/bioDS/beast-phylonco/commit/9c058c40ec61966b4ac5d51e27d83a3db20a0240

kche309 commented 2 years ago

Unit testing is underway