mdbarnesUCSD

Results 3 issues of mdbarnesUCSD

- Add support for VCF inputs for SV matrix generation - Update README

enhancement

- Apply black automatic formatting - Apply SigProfilerPlotting's process_input to input data

* Use SigProfilerPlottings custom_text_upper and custom_text_middle to include the stability and mutation count to the de novo signature plots for SBS4608.