First commit refactoring command line interface

parklab / xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

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First commit refactoring command line interface #111

Closed corinsexton closed 5 months ago

corinsexton commented 5 months ago

This PR is the first commit to the new CLI for xTea.

Major revisions include a newly trained genotyping module in ONNX version to overcome sklearn and DF versioning issues. This CLI version only supports mosaic and germline modes and is not tested to give identical output to the original xTea software.

corinsexton commented 5 months ago

First commit into CLI branch.